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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: 1-150806209-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=1&pos=150806209&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "1",
"pos": 150806209,
"ref": "G",
"alt": "A",
"effect": "missense_variant",
"transcript": "NM_000396.4",
"consequences": [
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CTSK",
"gene_hgnc_id": 2536,
"hgvs_c": "c.136C>T",
"hgvs_p": "p.Arg46Trp",
"transcript": "NM_000396.4",
"protein_id": "NP_000387.1",
"transcript_support_level": null,
"aa_start": 46,
"aa_end": null,
"aa_length": 329,
"cds_start": 136,
"cds_end": null,
"cds_length": 990,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000271651.8",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_000396.4"
},
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CTSK",
"gene_hgnc_id": 2536,
"hgvs_c": "c.136C>T",
"hgvs_p": "p.Arg46Trp",
"transcript": "ENST00000271651.8",
"protein_id": "ENSP00000271651.3",
"transcript_support_level": 1,
"aa_start": 46,
"aa_end": null,
"aa_length": 329,
"cds_start": 136,
"cds_end": null,
"cds_length": 990,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_000396.4",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000271651.8"
},
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CTSK",
"gene_hgnc_id": 2536,
"hgvs_c": "c.313C>T",
"hgvs_p": "p.Arg105Trp",
"transcript": "ENST00000443913.2",
"protein_id": "ENSP00000405083.2",
"transcript_support_level": 3,
"aa_start": 105,
"aa_end": null,
"aa_length": 388,
"cds_start": 313,
"cds_end": null,
"cds_length": 1167,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000443913.2"
},
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CTSK",
"gene_hgnc_id": 2536,
"hgvs_c": "c.178C>T",
"hgvs_p": "p.Arg60Trp",
"transcript": "ENST00000677887.1",
"protein_id": "ENSP00000503876.1",
"transcript_support_level": null,
"aa_start": 60,
"aa_end": null,
"aa_length": 343,
"cds_start": 178,
"cds_end": null,
"cds_length": 1032,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000677887.1"
},
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CTSK",
"gene_hgnc_id": 2536,
"hgvs_c": "c.172C>T",
"hgvs_p": "p.Arg58Trp",
"transcript": "ENST00000678337.1",
"protein_id": "ENSP00000504759.1",
"transcript_support_level": null,
"aa_start": 58,
"aa_end": null,
"aa_length": 341,
"cds_start": 172,
"cds_end": null,
"cds_length": 1026,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000678337.1"
},
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CTSK",
"gene_hgnc_id": 2536,
"hgvs_c": "c.136C>T",
"hgvs_p": "p.Arg46Trp",
"transcript": "ENST00000962229.1",
"protein_id": "ENSP00000632288.1",
"transcript_support_level": null,
"aa_start": 46,
"aa_end": null,
"aa_length": 337,
"cds_start": 136,
"cds_end": null,
"cds_length": 1014,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000962229.1"
},
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CTSK",
"gene_hgnc_id": 2536,
"hgvs_c": "c.151C>T",
"hgvs_p": "p.Arg51Trp",
"transcript": "ENST00000962227.1",
"protein_id": "ENSP00000632286.1",
"transcript_support_level": null,
"aa_start": 51,
"aa_end": null,
"aa_length": 334,
"cds_start": 151,
"cds_end": null,
"cds_length": 1005,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000962227.1"
},
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CTSK",
"gene_hgnc_id": 2536,
"hgvs_c": "c.136C>T",
"hgvs_p": "p.Arg46Trp",
"transcript": "ENST00000676970.1",
"protein_id": "ENSP00000503832.1",
"transcript_support_level": null,
"aa_start": 46,
"aa_end": null,
"aa_length": 333,
"cds_start": 136,
"cds_end": null,
"cds_length": 1002,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000676970.1"
},
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CTSK",
"gene_hgnc_id": 2536,
"hgvs_c": "c.136C>T",
"hgvs_p": "p.Arg46Trp",
"transcript": "ENST00000676751.1",
"protein_id": "ENSP00000502964.1",
"transcript_support_level": null,
"aa_start": 46,
"aa_end": null,
"aa_length": 330,
"cds_start": 136,
"cds_end": null,
"cds_length": 993,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000676751.1"
},
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CTSK",
"gene_hgnc_id": 2536,
"hgvs_c": "c.136C>T",
"hgvs_p": "p.Arg46Trp",
"transcript": "ENST00000676824.1",
"protein_id": "ENSP00000504176.1",
"transcript_support_level": null,
"aa_start": 46,
"aa_end": null,
"aa_length": 329,
"cds_start": 136,
"cds_end": null,
"cds_length": 990,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000676824.1"
},
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CTSK",
"gene_hgnc_id": 2536,
"hgvs_c": "c.136C>T",
"hgvs_p": "p.Arg46Trp",
"transcript": "ENST00000676966.1",
"protein_id": "ENSP00000503723.1",
"transcript_support_level": null,
"aa_start": 46,
"aa_end": null,
"aa_length": 329,
"cds_start": 136,
"cds_end": null,
"cds_length": 990,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000676966.1"
},
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CTSK",
"gene_hgnc_id": 2536,
"hgvs_c": "c.136C>T",
"hgvs_p": "p.Arg46Trp",
"transcript": "ENST00000962228.1",
"protein_id": "ENSP00000632287.1",
"transcript_support_level": null,
"aa_start": 46,
"aa_end": null,
"aa_length": 329,
"cds_start": 136,
"cds_end": null,
"cds_length": 990,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000962228.1"
},
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CTSK",
"gene_hgnc_id": 2536,
"hgvs_c": "c.136C>T",
"hgvs_p": "p.Arg46Trp",
"transcript": "ENST00000962230.1",
"protein_id": "ENSP00000632289.1",
"transcript_support_level": null,
"aa_start": 46,
"aa_end": null,
"aa_length": 329,
"cds_start": 136,
"cds_end": null,
"cds_length": 990,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000962230.1"
},
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CTSK",
"gene_hgnc_id": 2536,
"hgvs_c": "c.49C>T",
"hgvs_p": "p.Arg17Trp",
"transcript": "ENST00000962226.1",
"protein_id": "ENSP00000632285.1",
"transcript_support_level": null,
"aa_start": 17,
"aa_end": null,
"aa_length": 300,
"cds_start": 49,
"cds_end": null,
"cds_length": 903,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000962226.1"
},
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CTSK",
"gene_hgnc_id": 2536,
"hgvs_c": "c.136C>T",
"hgvs_p": "p.Arg46Trp",
"transcript": "ENST00000679260.1",
"protein_id": "ENSP00000504534.1",
"transcript_support_level": null,
"aa_start": 46,
"aa_end": null,
"aa_length": 256,
"cds_start": 136,
"cds_end": null,
"cds_length": 771,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000679260.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "CTSK",
"gene_hgnc_id": 2536,
"hgvs_c": "c.121-193C>T",
"hgvs_p": null,
"transcript": "ENST00000676716.1",
"protein_id": "ENSP00000504737.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 288,
"cds_start": null,
"cds_end": null,
"cds_length": 867,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000676716.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "CTSK",
"gene_hgnc_id": 2536,
"hgvs_c": "c.120+477C>T",
"hgvs_p": null,
"transcript": "ENST00000923236.1",
"protein_id": "ENSP00000593295.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 236,
"cds_start": null,
"cds_end": null,
"cds_length": 711,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000923236.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CTSK",
"gene_hgnc_id": 2536,
"hgvs_c": "n.3205C>T",
"hgvs_p": null,
"transcript": "ENST00000480670.2",
"protein_id": null,
"transcript_support_level": 3,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "retained_intron",
"feature": "ENST00000480670.2"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CTSK",
"gene_hgnc_id": 2536,
"hgvs_c": "n.136C>T",
"hgvs_p": null,
"transcript": "ENST00000676680.1",
"protein_id": "ENSP00000503270.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "nonsense_mediated_decay",
"feature": "ENST00000676680.1"
},
{
"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": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CTSK",
"gene_hgnc_id": 2536,
"hgvs_c": "n.1962C>T",
"hgvs_p": null,
"transcript": "ENST00000677330.1",
"protein_id": null,
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "retained_intron",
"feature": "ENST00000677330.1"
},
{
"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": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CTSK",
"gene_hgnc_id": 2536,
"hgvs_c": "n.*28C>T",
"hgvs_p": null,
"transcript": "ENST00000678275.1",
"protein_id": "ENSP00000504796.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "nonsense_mediated_decay",
"feature": "ENST00000678275.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CTSK",
"gene_hgnc_id": 2536,
"hgvs_c": "n.1113C>T",
"hgvs_p": null,
"transcript": "ENST00000678725.1",
"protein_id": null,
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "retained_intron",
"feature": "ENST00000678725.1"
},
{
"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": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CTSK",
"gene_hgnc_id": 2536,
"hgvs_c": "n.721C>T",
"hgvs_p": null,
"transcript": "ENST00000679090.1",
"protein_id": null,
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
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"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "retained_intron",
"feature": "ENST00000679090.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CTSK",
"gene_hgnc_id": 2536,
"hgvs_c": "n.1477C>T",
"hgvs_p": null,
"transcript": "ENST00000679148.1",
"protein_id": null,
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
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"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "retained_intron",
"feature": "ENST00000679148.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CTSK",
"gene_hgnc_id": 2536,
"hgvs_c": "n.2497C>T",
"hgvs_p": null,
"transcript": "ENST00000679171.1",
"protein_id": null,
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
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"cdna_length": null,
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"mane_plus": null,
"biotype": "retained_intron",
"feature": "ENST00000679171.1"
},
{
"aa_ref": null,
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"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CTSK",
"gene_hgnc_id": 2536,
"hgvs_c": "n.*28C>T",
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"transcript": "ENST00000678275.1",
"protein_id": "ENSP00000504796.1",
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"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "nonsense_mediated_decay",
"feature": "ENST00000678275.1"
},
{
"aa_ref": null,
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"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"upstream_gene_variant"
],
"exon_rank": null,
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"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CTSK",
"gene_hgnc_id": 2536,
"hgvs_c": "n.-98C>T",
"hgvs_p": null,
"transcript": "ENST00000677611.1",
"protein_id": null,
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"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "retained_intron",
"feature": "ENST00000677611.1"
}
],
"gene_symbol": "CTSK",
"gene_hgnc_id": 2536,
"dbsnp": "rs371277428",
"frequency_reference_population": 0.000019208892,
"hom_count_reference_population": 0,
"allele_count_reference_population": 31,
"gnomad_exomes_af": 0.0000205237,
"gnomad_genomes_af": 0.00000657428,
"gnomad_exomes_ac": 30,
"gnomad_genomes_ac": 1,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.9429975152015686,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.3100000023841858,
"splice_prediction_selected": "Uncertain_significance",
"splice_source_selected": "max_spliceai",
"revel_score": 0.847,
"revel_prediction": "Pathogenic",
"alphamissense_score": 0.7386,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.41,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 1.446,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0.31,
"spliceai_max_prediction": "Uncertain_significance",
"dbscsnv_ada_score": null,
"dbscsnv_ada_prediction": null,
"apogee2_score": null,
"apogee2_prediction": null,
"mitotip_score": null,
"mitotip_prediction": null,
"acmg_score": 16,
"acmg_classification": "Pathogenic",
"acmg_criteria": "PM1,PM5,PP3_Strong,PP5_Very_Strong",
"acmg_by_gene": [
{
"score": 16,
"benign_score": 0,
"pathogenic_score": 16,
"criteria": [
"PM1",
"PM5",
"PP3_Strong",
"PP5_Very_Strong"
],
"verdict": "Pathogenic",
"transcript": "NM_000396.4",
"gene_symbol": "CTSK",
"hgnc_id": 2536,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.136C>T",
"hgvs_p": "p.Arg46Trp"
}
],
"clinvar_disease": "Pyknodysostosis,not provided",
"clinvar_classification": "Pathogenic/Likely pathogenic",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "P:5 LP:1",
"phenotype_combined": "Pyknodysostosis|not provided",
"pathogenicity_classification_combined": "Pathogenic/Likely pathogenic",
"custom_annotations": null
}
],
"message": null
}