← Back to variant description
GeneBe API Showcase
This page demonstrates how to use the GeneBe API to query variant information. The API provides programmatic access to genomic annotations and variant data.
API presented here should be used for checking single variants. If you want to check many variants at once, please use other API endpoints that you will find in the documentation.
Documentation & Advanced Usage
• Complete API documentation:docs.genebe.net/docs/api/overview/
• Interactive endpoint tester:api.genebe.net/cloud/gb-api-doc/swagger-ui/
• Python client for pandas:pypi.org/project/genebe/
• Java CLI for VCF files:github.com/pstawinski/genebe-cli
• All tools documented at:docs.genebe.net
API Request Examples for Variant: 2-127639336-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=2&pos=127639336&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "2",
"pos": 127639336,
"ref": "G",
"alt": "A",
"effect": "missense_variant",
"transcript": "NM_001161403.3",
"consequences": [
{
"aa_ref": "S",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LIMS2",
"gene_hgnc_id": 16084,
"hgvs_c": "c.971C>T",
"hgvs_p": "p.Ser324Leu",
"transcript": "NM_001161403.3",
"protein_id": "NP_001154875.1",
"transcript_support_level": null,
"aa_start": 324,
"aa_end": null,
"aa_length": 341,
"cds_start": 971,
"cds_end": null,
"cds_length": 1026,
"cdna_start": 1477,
"cdna_end": null,
"cdna_length": 2387,
"mane_select": "ENST00000355119.9",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "L",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LIMS2",
"gene_hgnc_id": 16084,
"hgvs_c": "c.971C>T",
"hgvs_p": "p.Ser324Leu",
"transcript": "ENST00000355119.9",
"protein_id": "ENSP00000347240.4",
"transcript_support_level": 1,
"aa_start": 324,
"aa_end": null,
"aa_length": 341,
"cds_start": 971,
"cds_end": null,
"cds_length": 1026,
"cdna_start": 1477,
"cdna_end": null,
"cdna_length": 2387,
"mane_select": "NM_001161403.3",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LIMS2",
"gene_hgnc_id": 16084,
"hgvs_c": "c.1043C>T",
"hgvs_p": "p.Ser348Leu",
"transcript": "ENST00000324938.9",
"protein_id": "ENSP00000326888.5",
"transcript_support_level": 1,
"aa_start": 348,
"aa_end": null,
"aa_length": 365,
"cds_start": 1043,
"cds_end": null,
"cds_length": 1098,
"cdna_start": 1201,
"cdna_end": null,
"cdna_length": 2111,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LIMS2",
"gene_hgnc_id": 16084,
"hgvs_c": "c.956C>T",
"hgvs_p": "p.Ser319Leu",
"transcript": "ENST00000409455.5",
"protein_id": "ENSP00000386383.1",
"transcript_support_level": 1,
"aa_start": 319,
"aa_end": null,
"aa_length": 336,
"cds_start": 956,
"cds_end": null,
"cds_length": 1011,
"cdna_start": 1592,
"cdna_end": null,
"cdna_length": 2500,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LIMS2",
"gene_hgnc_id": 16084,
"hgvs_c": "c.956C>T",
"hgvs_p": "p.Ser319Leu",
"transcript": "ENST00000410011.5",
"protein_id": "ENSP00000387002.1",
"transcript_support_level": 1,
"aa_start": 319,
"aa_end": null,
"aa_length": 336,
"cds_start": 956,
"cds_end": null,
"cds_length": 1011,
"cdna_start": 1427,
"cdna_end": null,
"cdna_length": 2335,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LIMS2",
"gene_hgnc_id": 16084,
"hgvs_c": "c.515C>T",
"hgvs_p": "p.Ser172Leu",
"transcript": "ENST00000409754.5",
"protein_id": "ENSP00000386345.1",
"transcript_support_level": 1,
"aa_start": 172,
"aa_end": null,
"aa_length": 189,
"cds_start": 515,
"cds_end": null,
"cds_length": 570,
"cdna_start": 710,
"cdna_end": null,
"cdna_length": 1620,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LIMS2",
"gene_hgnc_id": 16084,
"hgvs_c": "c.1043C>T",
"hgvs_p": "p.Ser348Leu",
"transcript": "NM_017980.5",
"protein_id": "NP_060450.2",
"transcript_support_level": null,
"aa_start": 348,
"aa_end": null,
"aa_length": 365,
"cds_start": 1043,
"cds_end": null,
"cds_length": 1098,
"cdna_start": 1248,
"cdna_end": null,
"cdna_length": 2158,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LIMS2",
"gene_hgnc_id": 16084,
"hgvs_c": "c.1037C>T",
"hgvs_p": "p.Ser346Leu",
"transcript": "NM_001136037.4",
"protein_id": "NP_001129509.2",
"transcript_support_level": null,
"aa_start": 346,
"aa_end": null,
"aa_length": 363,
"cds_start": 1037,
"cds_end": null,
"cds_length": 1092,
"cdna_start": 1543,
"cdna_end": null,
"cdna_length": 2453,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LIMS2",
"gene_hgnc_id": 16084,
"hgvs_c": "c.1037C>T",
"hgvs_p": "p.Ser346Leu",
"transcript": "ENST00000545738.6",
"protein_id": "ENSP00000443794.2",
"transcript_support_level": 5,
"aa_start": 346,
"aa_end": null,
"aa_length": 363,
"cds_start": 1037,
"cds_end": null,
"cds_length": 1092,
"cdna_start": 1115,
"cdna_end": null,
"cdna_length": 1730,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LIMS2",
"gene_hgnc_id": 16084,
"hgvs_c": "c.956C>T",
"hgvs_p": "p.Ser319Leu",
"transcript": "NM_001161404.2",
"protein_id": "NP_001154876.1",
"transcript_support_level": null,
"aa_start": 319,
"aa_end": null,
"aa_length": 336,
"cds_start": 956,
"cds_end": null,
"cds_length": 1011,
"cdna_start": 1427,
"cdna_end": null,
"cdna_length": 2337,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LIMS2",
"gene_hgnc_id": 16084,
"hgvs_c": "c.956C>T",
"hgvs_p": "p.Ser319Leu",
"transcript": "ENST00000409808.6",
"protein_id": "ENSP00000386637.2",
"transcript_support_level": 5,
"aa_start": 319,
"aa_end": null,
"aa_length": 336,
"cds_start": 956,
"cds_end": null,
"cds_length": 1011,
"cdna_start": 1407,
"cdna_end": null,
"cdna_length": 2315,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LIMS2",
"gene_hgnc_id": 16084,
"hgvs_c": "c.515C>T",
"hgvs_p": "p.Ser172Leu",
"transcript": "NM_001256542.2",
"protein_id": "NP_001243471.1",
"transcript_support_level": null,
"aa_start": 172,
"aa_end": null,
"aa_length": 189,
"cds_start": 515,
"cds_end": null,
"cds_length": 570,
"cdna_start": 829,
"cdna_end": null,
"cdna_length": 1739,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LIMS2",
"gene_hgnc_id": 16084,
"hgvs_c": "c.515C>T",
"hgvs_p": "p.Ser172Leu",
"transcript": "ENST00000409254.1",
"protein_id": "ENSP00000386907.1",
"transcript_support_level": 3,
"aa_start": 172,
"aa_end": null,
"aa_length": 189,
"cds_start": 515,
"cds_end": null,
"cds_length": 570,
"cdna_start": 728,
"cdna_end": null,
"cdna_length": 867,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LIMS2",
"gene_hgnc_id": 16084,
"hgvs_c": "c.515C>T",
"hgvs_p": "p.Ser172Leu",
"transcript": "ENST00000409286.5",
"protein_id": "ENSP00000386252.1",
"transcript_support_level": 2,
"aa_start": 172,
"aa_end": null,
"aa_length": 189,
"cds_start": 515,
"cds_end": null,
"cds_length": 570,
"cdna_start": 768,
"cdna_end": null,
"cdna_length": 1678,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LIMS2",
"gene_hgnc_id": 16084,
"hgvs_c": "c.515C>T",
"hgvs_p": "p.Ser172Leu",
"transcript": "ENST00000410038.5",
"protein_id": "ENSP00000386570.1",
"transcript_support_level": 2,
"aa_start": 172,
"aa_end": null,
"aa_length": 189,
"cds_start": 515,
"cds_end": null,
"cds_length": 570,
"cdna_start": 829,
"cdna_end": null,
"cdna_length": 1695,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LIMS2",
"gene_hgnc_id": 16084,
"hgvs_c": "c.452C>T",
"hgvs_p": "p.Ser151Leu",
"transcript": "ENST00000426981.5",
"protein_id": "ENSP00000397253.1",
"transcript_support_level": 3,
"aa_start": 151,
"aa_end": null,
"aa_length": 168,
"cds_start": 452,
"cds_end": null,
"cds_length": 507,
"cdna_start": 454,
"cdna_end": null,
"cdna_length": 1409,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LIMS2",
"gene_hgnc_id": 16084,
"hgvs_c": "c.1028C>T",
"hgvs_p": "p.Ser343Leu",
"transcript": "XM_047444963.1",
"protein_id": "XP_047300919.1",
"transcript_support_level": null,
"aa_start": 343,
"aa_end": null,
"aa_length": 360,
"cds_start": 1028,
"cds_end": null,
"cds_length": 1083,
"cdna_start": 1215,
"cdna_end": null,
"cdna_length": 2125,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LIMS2",
"gene_hgnc_id": 16084,
"hgvs_c": "c.956C>T",
"hgvs_p": "p.Ser319Leu",
"transcript": "XM_024452983.2",
"protein_id": "XP_024308751.1",
"transcript_support_level": null,
"aa_start": 319,
"aa_end": null,
"aa_length": 336,
"cds_start": 956,
"cds_end": null,
"cds_length": 1011,
"cdna_start": 1279,
"cdna_end": null,
"cdna_length": 2189,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LIMS2",
"gene_hgnc_id": 16084,
"hgvs_c": "c.920C>T",
"hgvs_p": "p.Ser307Leu",
"transcript": "XM_011511453.2",
"protein_id": "XP_011509755.1",
"transcript_support_level": null,
"aa_start": 307,
"aa_end": null,
"aa_length": 324,
"cds_start": 920,
"cds_end": null,
"cds_length": 975,
"cdna_start": 1125,
"cdna_end": null,
"cdna_length": 2035,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LIMS2",
"gene_hgnc_id": 16084,
"hgvs_c": "c.848C>T",
"hgvs_p": "p.Ser283Leu",
"transcript": "XM_047444970.1",
"protein_id": "XP_047300926.1",
"transcript_support_level": null,
"aa_start": 283,
"aa_end": null,
"aa_length": 300,
"cds_start": 848,
"cds_end": null,
"cds_length": 903,
"cdna_start": 1354,
"cdna_end": null,
"cdna_length": 2264,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LIMS2",
"gene_hgnc_id": 16084,
"hgvs_c": "c.764C>T",
"hgvs_p": "p.Ser255Leu",
"transcript": "XM_005263710.3",
"protein_id": "XP_005263767.1",
"transcript_support_level": null,
"aa_start": 255,
"aa_end": null,
"aa_length": 272,
"cds_start": 764,
"cds_end": null,
"cds_length": 819,
"cdna_start": 1317,
"cdna_end": null,
"cdna_length": 2227,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LIMS2",
"gene_hgnc_id": 16084,
"hgvs_c": "c.710C>T",
"hgvs_p": "p.Ser237Leu",
"transcript": "XM_047444972.1",
"protein_id": "XP_047300928.1",
"transcript_support_level": null,
"aa_start": 237,
"aa_end": null,
"aa_length": 254,
"cds_start": 710,
"cds_end": null,
"cds_length": 765,
"cdna_start": 805,
"cdna_end": null,
"cdna_length": 1715,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LIMS2",
"gene_hgnc_id": 16084,
"hgvs_c": "c.662C>T",
"hgvs_p": "p.Ser221Leu",
"transcript": "XM_017004469.2",
"protein_id": "XP_016859958.1",
"transcript_support_level": null,
"aa_start": 221,
"aa_end": null,
"aa_length": 238,
"cds_start": 662,
"cds_end": null,
"cds_length": 717,
"cdna_start": 695,
"cdna_end": null,
"cdna_length": 1605,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LIMS2",
"gene_hgnc_id": 16084,
"hgvs_c": "c.623C>T",
"hgvs_p": "p.Ser208Leu",
"transcript": "XM_006712627.5",
"protein_id": "XP_006712690.1",
"transcript_support_level": null,
"aa_start": 208,
"aa_end": null,
"aa_length": 225,
"cds_start": 623,
"cds_end": null,
"cds_length": 678,
"cdna_start": 1129,
"cdna_end": null,
"cdna_length": 2039,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LIMS2",
"gene_hgnc_id": 16084,
"hgvs_c": "c.515C>T",
"hgvs_p": "p.Ser172Leu",
"transcript": "XM_024452985.2",
"protein_id": "XP_024308753.1",
"transcript_support_level": null,
"aa_start": 172,
"aa_end": null,
"aa_length": 189,
"cds_start": 515,
"cds_end": null,
"cds_length": 570,
"cdna_start": 752,
"cdna_end": null,
"cdna_length": 1662,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LIMS2",
"gene_hgnc_id": 16084,
"hgvs_c": "c.515C>T",
"hgvs_p": "p.Ser172Leu",
"transcript": "XM_024452986.2",
"protein_id": "XP_024308754.1",
"transcript_support_level": null,
"aa_start": 172,
"aa_end": null,
"aa_length": 189,
"cds_start": 515,
"cds_end": null,
"cds_length": 570,
"cdna_start": 716,
"cdna_end": null,
"cdna_length": 1626,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LIMS2",
"gene_hgnc_id": 16084,
"hgvs_c": "c.515C>T",
"hgvs_p": "p.Ser172Leu",
"transcript": "XM_047444975.1",
"protein_id": "XP_047300931.1",
"transcript_support_level": null,
"aa_start": 172,
"aa_end": null,
"aa_length": 189,
"cds_start": 515,
"cds_end": null,
"cds_length": 570,
"cdna_start": 2136,
"cdna_end": null,
"cdna_length": 3046,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LIMS2",
"gene_hgnc_id": 16084,
"hgvs_c": "c.515C>T",
"hgvs_p": "p.Ser172Leu",
"transcript": "XM_047444976.1",
"protein_id": "XP_047300932.1",
"transcript_support_level": null,
"aa_start": 172,
"aa_end": null,
"aa_length": 189,
"cds_start": 515,
"cds_end": null,
"cds_length": 570,
"cdna_start": 1841,
"cdna_end": null,
"cdna_length": 2751,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LIMS2",
"gene_hgnc_id": 16084,
"hgvs_c": "n.*181C>T",
"hgvs_p": null,
"transcript": "ENST00000413578.5",
"protein_id": "ENSP00000388611.1",
"transcript_support_level": 3,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 930,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LIMS2",
"gene_hgnc_id": 16084,
"hgvs_c": "n.1684C>T",
"hgvs_p": null,
"transcript": "ENST00000466410.5",
"protein_id": null,
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2592,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LIMS2",
"gene_hgnc_id": 16084,
"hgvs_c": "n.3896C>T",
"hgvs_p": null,
"transcript": "ENST00000469300.6",
"protein_id": null,
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 4807,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LIMS2",
"gene_hgnc_id": 16084,
"hgvs_c": "n.1359C>T",
"hgvs_p": null,
"transcript": "ENST00000476932.5",
"protein_id": null,
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2269,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LIMS2",
"gene_hgnc_id": 16084,
"hgvs_c": "n.1191C>T",
"hgvs_p": null,
"transcript": "ENST00000484252.5",
"protein_id": null,
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2099,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LIMS2",
"gene_hgnc_id": 16084,
"hgvs_c": "n.227C>T",
"hgvs_p": null,
"transcript": "ENST00000494613.5",
"protein_id": null,
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1137,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LIMS2",
"gene_hgnc_id": 16084,
"hgvs_c": "n.*181C>T",
"hgvs_p": null,
"transcript": "ENST00000413578.5",
"protein_id": "ENSP00000388611.1",
"transcript_support_level": 3,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 930,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "LIMS2",
"gene_hgnc_id": 16084,
"dbsnp": "rs377574169",
"frequency_reference_population": 0.00005948346,
"hom_count_reference_population": 0,
"allele_count_reference_population": 96,
"gnomad_exomes_af": 0.0000410494,
"gnomad_genomes_af": 0.000236466,
"gnomad_exomes_ac": 60,
"gnomad_genomes_ac": 36,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.034286439418792725,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.245,
"revel_prediction": "Benign",
"alphamissense_score": 0.1049,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.36,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 6.89,
"phylop100way_prediction": "Uncertain_significance",
"spliceai_max_score": 0,
"spliceai_max_prediction": "Benign",
"dbscsnv_ada_score": null,
"dbscsnv_ada_prediction": null,
"apogee2_score": null,
"apogee2_prediction": null,
"mitotip_score": null,
"mitotip_prediction": null,
"acmg_score": -4,
"acmg_classification": "Likely_benign",
"acmg_criteria": "BP4_Strong",
"acmg_by_gene": [
{
"score": -4,
"benign_score": 4,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong"
],
"verdict": "Likely_benign",
"transcript": "NM_001161403.3",
"gene_symbol": "LIMS2",
"hgnc_id": 16084,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR,Unknown",
"hgvs_c": "c.971C>T",
"hgvs_p": "p.Ser324Leu"
}
],
"clinvar_disease": "Autosomal recessive limb-girdle muscular dystrophy type 2W",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "US:2",
"phenotype_combined": "Autosomal recessive limb-girdle muscular dystrophy type 2W",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}