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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: 1-31656405-G-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=1&pos=31656405&ref=G&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "1",
"pos": 31656405,
"ref": "G",
"alt": "T",
"effect": "missense_variant",
"transcript": "NM_001856.4",
"consequences": [
{
"aa_ref": "P",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 66,
"exon_rank_end": null,
"exon_count": 71,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL16A1",
"gene_hgnc_id": 2193,
"hgvs_c": "c.4096C>A",
"hgvs_p": "p.Pro1366Thr",
"transcript": "NM_001856.4",
"protein_id": "NP_001847.3",
"transcript_support_level": null,
"aa_start": 1366,
"aa_end": null,
"aa_length": 1604,
"cds_start": 4096,
"cds_end": null,
"cds_length": 4815,
"cdna_start": 4311,
"cdna_end": null,
"cdna_length": 5418,
"mane_select": "ENST00000373672.8",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001856.4"
},
{
"aa_ref": "P",
"aa_alt": "T",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 66,
"exon_rank_end": null,
"exon_count": 71,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL16A1",
"gene_hgnc_id": 2193,
"hgvs_c": "c.4096C>A",
"hgvs_p": "p.Pro1366Thr",
"transcript": "ENST00000373672.8",
"protein_id": "ENSP00000362776.3",
"transcript_support_level": 5,
"aa_start": 1366,
"aa_end": null,
"aa_length": 1604,
"cds_start": 4096,
"cds_end": null,
"cds_length": 4815,
"cdna_start": 4311,
"cdna_end": null,
"cdna_length": 5418,
"mane_select": "NM_001856.4",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000373672.8"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL16A1",
"gene_hgnc_id": 2193,
"hgvs_c": "n.1339C>A",
"hgvs_p": null,
"transcript": "ENST00000488897.5",
"protein_id": null,
"transcript_support_level": 1,
"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": 2423,
"mane_select": null,
"mane_plus": null,
"biotype": "retained_intron",
"feature": "ENST00000488897.5"
},
{
"aa_ref": "P",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 65,
"exon_rank_end": null,
"exon_count": 70,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL16A1",
"gene_hgnc_id": 2193,
"hgvs_c": "c.4051C>A",
"hgvs_p": "p.Pro1351Thr",
"transcript": "ENST00000873809.1",
"protein_id": "ENSP00000543868.1",
"transcript_support_level": null,
"aa_start": 1351,
"aa_end": null,
"aa_length": 1589,
"cds_start": 4051,
"cds_end": null,
"cds_length": 4770,
"cdna_start": 4275,
"cdna_end": null,
"cdna_length": 5385,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000873809.1"
},
{
"aa_ref": "P",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 63,
"exon_rank_end": null,
"exon_count": 68,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL16A1",
"gene_hgnc_id": 2193,
"hgvs_c": "c.3916C>A",
"hgvs_p": "p.Pro1306Thr",
"transcript": "ENST00000933935.1",
"protein_id": "ENSP00000603994.1",
"transcript_support_level": null,
"aa_start": 1306,
"aa_end": null,
"aa_length": 1544,
"cds_start": 3916,
"cds_end": null,
"cds_length": 4635,
"cdna_start": 4279,
"cdna_end": null,
"cdna_length": 5147,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000933935.1"
},
{
"aa_ref": "P",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 60,
"exon_rank_end": null,
"exon_count": 65,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL16A1",
"gene_hgnc_id": 2193,
"hgvs_c": "c.3772C>A",
"hgvs_p": "p.Pro1258Thr",
"transcript": "ENST00000873810.1",
"protein_id": "ENSP00000543869.1",
"transcript_support_level": null,
"aa_start": 1258,
"aa_end": null,
"aa_length": 1496,
"cds_start": 3772,
"cds_end": null,
"cds_length": 4491,
"cdna_start": 3987,
"cdna_end": null,
"cdna_length": 4855,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000873810.1"
},
{
"aa_ref": "P",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL16A1",
"gene_hgnc_id": 2193,
"hgvs_c": "c.667C>A",
"hgvs_p": "p.Pro223Thr",
"transcript": "ENST00000440437.1",
"protein_id": "ENSP00000390281.1",
"transcript_support_level": 5,
"aa_start": 223,
"aa_end": null,
"aa_length": 223,
"cds_start": 667,
"cds_end": null,
"cds_length": 672,
"cdna_start": 667,
"cdna_end": null,
"cdna_length": 672,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000440437.1"
},
{
"aa_ref": "P",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 65,
"exon_rank_end": null,
"exon_count": 70,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL16A1",
"gene_hgnc_id": 2193,
"hgvs_c": "c.4063C>A",
"hgvs_p": "p.Pro1355Thr",
"transcript": "XM_017000338.2",
"protein_id": "XP_016855827.1",
"transcript_support_level": null,
"aa_start": 1355,
"aa_end": null,
"aa_length": 1593,
"cds_start": 4063,
"cds_end": null,
"cds_length": 4782,
"cdna_start": 4278,
"cdna_end": null,
"cdna_length": 5385,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_017000338.2"
},
{
"aa_ref": "P",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 65,
"exon_rank_end": null,
"exon_count": 70,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL16A1",
"gene_hgnc_id": 2193,
"hgvs_c": "c.4060C>A",
"hgvs_p": "p.Pro1354Thr",
"transcript": "XM_017000339.2",
"protein_id": "XP_016855828.1",
"transcript_support_level": null,
"aa_start": 1354,
"aa_end": null,
"aa_length": 1592,
"cds_start": 4060,
"cds_end": null,
"cds_length": 4779,
"cdna_start": 4275,
"cdna_end": null,
"cdna_length": 5382,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_017000339.2"
},
{
"aa_ref": "P",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 65,
"exon_rank_end": null,
"exon_count": 70,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL16A1",
"gene_hgnc_id": 2193,
"hgvs_c": "c.4051C>A",
"hgvs_p": "p.Pro1351Thr",
"transcript": "XM_011540722.2",
"protein_id": "XP_011539024.1",
"transcript_support_level": null,
"aa_start": 1351,
"aa_end": null,
"aa_length": 1589,
"cds_start": 4051,
"cds_end": null,
"cds_length": 4770,
"cdna_start": 4266,
"cdna_end": null,
"cdna_length": 5373,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_011540722.2"
},
{
"aa_ref": "P",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 65,
"exon_rank_end": null,
"exon_count": 70,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL16A1",
"gene_hgnc_id": 2193,
"hgvs_c": "c.4048C>A",
"hgvs_p": "p.Pro1350Thr",
"transcript": "XM_005270481.2",
"protein_id": "XP_005270538.1",
"transcript_support_level": null,
"aa_start": 1350,
"aa_end": null,
"aa_length": 1588,
"cds_start": 4048,
"cds_end": null,
"cds_length": 4767,
"cdna_start": 4263,
"cdna_end": null,
"cdna_length": 5370,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_005270481.2"
},
{
"aa_ref": "P",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 64,
"exon_rank_end": null,
"exon_count": 69,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL16A1",
"gene_hgnc_id": 2193,
"hgvs_c": "c.4003C>A",
"hgvs_p": "p.Pro1335Thr",
"transcript": "XM_011540723.2",
"protein_id": "XP_011539025.1",
"transcript_support_level": null,
"aa_start": 1335,
"aa_end": null,
"aa_length": 1573,
"cds_start": 4003,
"cds_end": null,
"cds_length": 4722,
"cdna_start": 4218,
"cdna_end": null,
"cdna_length": 5325,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_011540723.2"
},
{
"aa_ref": "P",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 65,
"exon_rank_end": null,
"exon_count": 70,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL16A1",
"gene_hgnc_id": 2193,
"hgvs_c": "c.3973C>A",
"hgvs_p": "p.Pro1325Thr",
"transcript": "XM_011540724.2",
"protein_id": "XP_011539026.1",
"transcript_support_level": null,
"aa_start": 1325,
"aa_end": null,
"aa_length": 1563,
"cds_start": 3973,
"cds_end": null,
"cds_length": 4692,
"cdna_start": 4188,
"cdna_end": null,
"cdna_length": 5295,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_011540724.2"
},
{
"aa_ref": "P",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 63,
"exon_rank_end": null,
"exon_count": 68,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL16A1",
"gene_hgnc_id": 2193,
"hgvs_c": "c.3967C>A",
"hgvs_p": "p.Pro1323Thr",
"transcript": "XM_047446431.1",
"protein_id": "XP_047302387.1",
"transcript_support_level": null,
"aa_start": 1323,
"aa_end": null,
"aa_length": 1561,
"cds_start": 3967,
"cds_end": null,
"cds_length": 4686,
"cdna_start": 4182,
"cdna_end": null,
"cdna_length": 5289,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047446431.1"
},
{
"aa_ref": "P",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 64,
"exon_rank_end": null,
"exon_count": 69,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL16A1",
"gene_hgnc_id": 2193,
"hgvs_c": "c.3928C>A",
"hgvs_p": "p.Pro1310Thr",
"transcript": "XM_047446432.1",
"protein_id": "XP_047302388.1",
"transcript_support_level": null,
"aa_start": 1310,
"aa_end": null,
"aa_length": 1548,
"cds_start": 3928,
"cds_end": null,
"cds_length": 4647,
"cdna_start": 4143,
"cdna_end": null,
"cdna_length": 5250,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047446432.1"
},
{
"aa_ref": "P",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 62,
"exon_rank_end": null,
"exon_count": 67,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL16A1",
"gene_hgnc_id": 2193,
"hgvs_c": "c.3844C>A",
"hgvs_p": "p.Pro1282Thr",
"transcript": "XM_047446435.1",
"protein_id": "XP_047302391.1",
"transcript_support_level": null,
"aa_start": 1282,
"aa_end": null,
"aa_length": 1520,
"cds_start": 3844,
"cds_end": null,
"cds_length": 4563,
"cdna_start": 4059,
"cdna_end": null,
"cdna_length": 5166,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047446435.1"
},
{
"aa_ref": "P",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 62,
"exon_rank_end": null,
"exon_count": 67,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL16A1",
"gene_hgnc_id": 2193,
"hgvs_c": "c.3535C>A",
"hgvs_p": "p.Pro1179Thr",
"transcript": "XM_047446439.1",
"protein_id": "XP_047302395.1",
"transcript_support_level": null,
"aa_start": 1179,
"aa_end": null,
"aa_length": 1417,
"cds_start": 3535,
"cds_end": null,
"cds_length": 4254,
"cdna_start": 3924,
"cdna_end": null,
"cdna_length": 5031,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047446439.1"
},
{
"aa_ref": "P",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 56,
"exon_rank_end": null,
"exon_count": 61,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL16A1",
"gene_hgnc_id": 2193,
"hgvs_c": "c.3190C>A",
"hgvs_p": "p.Pro1064Thr",
"transcript": "XM_011540727.3",
"protein_id": "XP_011539029.1",
"transcript_support_level": null,
"aa_start": 1064,
"aa_end": null,
"aa_length": 1302,
"cds_start": 3190,
"cds_end": null,
"cds_length": 3909,
"cdna_start": 3217,
"cdna_end": null,
"cdna_length": 4324,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_011540727.3"
},
{
"aa_ref": "P",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 44,
"exon_rank_end": null,
"exon_count": 49,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL16A1",
"gene_hgnc_id": 2193,
"hgvs_c": "c.2551C>A",
"hgvs_p": "p.Pro851Thr",
"transcript": "XM_011540728.3",
"protein_id": "XP_011539030.1",
"transcript_support_level": null,
"aa_start": 851,
"aa_end": null,
"aa_length": 1089,
"cds_start": 2551,
"cds_end": null,
"cds_length": 3270,
"cdna_start": 2700,
"cdna_end": null,
"cdna_length": 3807,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_011540728.3"
},
{
"aa_ref": "P",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 43,
"exon_rank_end": null,
"exon_count": 48,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL16A1",
"gene_hgnc_id": 2193,
"hgvs_c": "c.2515C>A",
"hgvs_p": "p.Pro839Thr",
"transcript": "XM_017000340.3",
"protein_id": "XP_016855829.1",
"transcript_support_level": null,
"aa_start": 839,
"aa_end": null,
"aa_length": 1077,
"cds_start": 2515,
"cds_end": null,
"cds_length": 3234,
"cdna_start": 2663,
"cdna_end": null,
"cdna_length": 3770,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_017000340.3"
},
{
"aa_ref": "P",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 43,
"exon_rank_end": null,
"exon_count": 48,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL16A1",
"gene_hgnc_id": 2193,
"hgvs_c": "c.2368C>A",
"hgvs_p": "p.Pro790Thr",
"transcript": "XM_017000341.2",
"protein_id": "XP_016855830.1",
"transcript_support_level": null,
"aa_start": 790,
"aa_end": null,
"aa_length": 1028,
"cds_start": 2368,
"cds_end": null,
"cds_length": 3087,
"cdna_start": 2452,
"cdna_end": null,
"cdna_length": 3559,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_017000341.2"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL16A1",
"gene_hgnc_id": 2193,
"hgvs_c": "n.1693C>A",
"hgvs_p": null,
"transcript": "ENST00000488128.6",
"protein_id": null,
"transcript_support_level": 5,
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{
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"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
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],
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{
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},
{
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],
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"feature": "ENST00000820351.1"
},
{
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"strand": true,
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"intron_variant"
],
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"gene_symbol": "PEF1-AS1",
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"feature": "NR_184311.1"
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{
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"strand": true,
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"intron_variant"
],
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"gene_symbol": "PEF1-AS1",
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},
{
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"intron_variant"
],
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"gene_symbol": "PEF1-AS1",
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"feature": "NR_184313.1"
},
{
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"strand": true,
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"intron_variant"
],
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"gene_symbol": "PEF1-AS1",
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"transcript": "NR_184314.1",
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"biotype": "pseudogene",
"feature": "NR_184314.1"
}
],
"gene_symbol": "COL16A1",
"gene_hgnc_id": 2193,
"dbsnp": "rs370207674",
"frequency_reference_population": 0.00003904923,
"hom_count_reference_population": 0,
"allele_count_reference_population": 63,
"gnomad_exomes_af": 0.0000403784,
"gnomad_genomes_af": 0.0000262864,
"gnomad_exomes_ac": 59,
"gnomad_genomes_ac": 4,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.29338598251342773,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.381,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": 0.0797,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.08,
"bayesdelnoaf_prediction": "Uncertain_significance",
"phylop100way_score": 1.882,
"phylop100way_prediction": "Benign",
"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": 1,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2,BP4",
"acmg_by_gene": [
{
"score": 1,
"benign_score": 1,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4"
],
"verdict": "Uncertain_significance",
"transcript": "NM_001856.4",
"gene_symbol": "COL16A1",
"hgnc_id": 2193,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.4096C>A",
"hgvs_p": "p.Pro1366Thr"
},
{
"score": 1,
"benign_score": 1,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000820353.1",
"gene_symbol": "PEF1-AS1",
"hgnc_id": 40154,
"effects": [
"non_coding_transcript_exon_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.730G>T",
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}
],
"clinvar_disease": "not specified",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"phenotype_combined": "not specified",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}