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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: 3-134175954-T-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=3&pos=134175954&ref=T&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "3",
"pos": 134175954,
"ref": "T",
"alt": "C",
"effect": "missense_variant",
"transcript": "NM_001005861.3",
"consequences": [
{
"aa_ref": "K",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RYK",
"gene_hgnc_id": 10481,
"hgvs_c": "c.1391A>G",
"hgvs_p": "p.Lys464Arg",
"transcript": "NM_002958.4",
"protein_id": "NP_002949.2",
"transcript_support_level": null,
"aa_start": 464,
"aa_end": null,
"aa_length": 607,
"cds_start": 1391,
"cds_end": null,
"cds_length": 1824,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000623711.4",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_002958.4"
},
{
"aa_ref": "K",
"aa_alt": "R",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RYK",
"gene_hgnc_id": 10481,
"hgvs_c": "c.1391A>G",
"hgvs_p": "p.Lys464Arg",
"transcript": "ENST00000623711.4",
"protein_id": "ENSP00000485095.1",
"transcript_support_level": 1,
"aa_start": 464,
"aa_end": null,
"aa_length": 607,
"cds_start": 1391,
"cds_end": null,
"cds_length": 1824,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_002958.4",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000623711.4"
},
{
"aa_ref": "K",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RYK",
"gene_hgnc_id": 10481,
"hgvs_c": "c.1400A>G",
"hgvs_p": "p.Lys467Arg",
"transcript": "ENST00000620660.4",
"protein_id": "ENSP00000478721.1",
"transcript_support_level": 1,
"aa_start": 467,
"aa_end": null,
"aa_length": 610,
"cds_start": 1400,
"cds_end": null,
"cds_length": 1833,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000620660.4"
},
{
"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": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RYK",
"gene_hgnc_id": 10481,
"hgvs_c": "n.3818A>G",
"hgvs_p": null,
"transcript": "ENST00000473208.5",
"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": null,
"mane_select": null,
"mane_plus": null,
"biotype": "retained_intron",
"feature": "ENST00000473208.5"
},
{
"aa_ref": "K",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RYK",
"gene_hgnc_id": 10481,
"hgvs_c": "c.1457A>G",
"hgvs_p": "p.Lys486Arg",
"transcript": "ENST00000946535.1",
"protein_id": "ENSP00000616594.1",
"transcript_support_level": null,
"aa_start": 486,
"aa_end": null,
"aa_length": 629,
"cds_start": 1457,
"cds_end": null,
"cds_length": 1890,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000946535.1"
},
{
"aa_ref": "K",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RYK",
"gene_hgnc_id": 10481,
"hgvs_c": "c.1448A>G",
"hgvs_p": "p.Lys483Arg",
"transcript": "ENST00000912304.1",
"protein_id": "ENSP00000582363.1",
"transcript_support_level": null,
"aa_start": 483,
"aa_end": null,
"aa_length": 626,
"cds_start": 1448,
"cds_end": null,
"cds_length": 1881,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000912304.1"
},
{
"aa_ref": "K",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RYK",
"gene_hgnc_id": 10481,
"hgvs_c": "c.1400A>G",
"hgvs_p": "p.Lys467Arg",
"transcript": "NM_001005861.3",
"protein_id": "NP_001005861.1",
"transcript_support_level": null,
"aa_start": 467,
"aa_end": null,
"aa_length": 610,
"cds_start": 1400,
"cds_end": null,
"cds_length": 1833,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001005861.3"
},
{
"aa_ref": "K",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RYK",
"gene_hgnc_id": 10481,
"hgvs_c": "c.1400A>G",
"hgvs_p": "p.Lys467Arg",
"transcript": "ENST00000907584.1",
"protein_id": "ENSP00000577643.1",
"transcript_support_level": null,
"aa_start": 467,
"aa_end": null,
"aa_length": 610,
"cds_start": 1400,
"cds_end": null,
"cds_length": 1833,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000907584.1"
},
{
"aa_ref": "K",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RYK",
"gene_hgnc_id": 10481,
"hgvs_c": "c.1400A>G",
"hgvs_p": "p.Lys467Arg",
"transcript": "ENST00000912303.1",
"protein_id": "ENSP00000582362.1",
"transcript_support_level": null,
"aa_start": 467,
"aa_end": null,
"aa_length": 610,
"cds_start": 1400,
"cds_end": null,
"cds_length": 1833,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000912303.1"
},
{
"aa_ref": "K",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RYK",
"gene_hgnc_id": 10481,
"hgvs_c": "c.1391A>G",
"hgvs_p": "p.Lys464Arg",
"transcript": "ENST00000907585.1",
"protein_id": "ENSP00000577644.1",
"transcript_support_level": null,
"aa_start": 464,
"aa_end": null,
"aa_length": 607,
"cds_start": 1391,
"cds_end": null,
"cds_length": 1824,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000907585.1"
},
{
"aa_ref": "K",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RYK",
"gene_hgnc_id": 10481,
"hgvs_c": "c.1313A>G",
"hgvs_p": "p.Lys438Arg",
"transcript": "ENST00000946538.1",
"protein_id": "ENSP00000616597.1",
"transcript_support_level": null,
"aa_start": 438,
"aa_end": null,
"aa_length": 581,
"cds_start": 1313,
"cds_end": null,
"cds_length": 1746,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000946538.1"
},
{
"aa_ref": "K",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RYK",
"gene_hgnc_id": 10481,
"hgvs_c": "c.1304A>G",
"hgvs_p": "p.Lys435Arg",
"transcript": "ENST00000912307.1",
"protein_id": "ENSP00000582366.1",
"transcript_support_level": null,
"aa_start": 435,
"aa_end": null,
"aa_length": 578,
"cds_start": 1304,
"cds_end": null,
"cds_length": 1737,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000912307.1"
},
{
"aa_ref": "K",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RYK",
"gene_hgnc_id": 10481,
"hgvs_c": "c.1265A>G",
"hgvs_p": "p.Lys422Arg",
"transcript": "ENST00000912305.1",
"protein_id": "ENSP00000582364.1",
"transcript_support_level": null,
"aa_start": 422,
"aa_end": null,
"aa_length": 565,
"cds_start": 1265,
"cds_end": null,
"cds_length": 1698,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000912305.1"
},
{
"aa_ref": "K",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RYK",
"gene_hgnc_id": 10481,
"hgvs_c": "c.1235A>G",
"hgvs_p": "p.Lys412Arg",
"transcript": "ENST00000946539.1",
"protein_id": "ENSP00000616598.1",
"transcript_support_level": null,
"aa_start": 412,
"aa_end": null,
"aa_length": 555,
"cds_start": 1235,
"cds_end": null,
"cds_length": 1668,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000946539.1"
},
{
"aa_ref": "K",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RYK",
"gene_hgnc_id": 10481,
"hgvs_c": "c.1211A>G",
"hgvs_p": "p.Lys404Arg",
"transcript": "ENST00000946530.1",
"protein_id": "ENSP00000616589.1",
"transcript_support_level": null,
"aa_start": 404,
"aa_end": null,
"aa_length": 547,
"cds_start": 1211,
"cds_end": null,
"cds_length": 1644,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000946530.1"
},
{
"aa_ref": "K",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RYK",
"gene_hgnc_id": 10481,
"hgvs_c": "c.1202A>G",
"hgvs_p": "p.Lys401Arg",
"transcript": "ENST00000946529.1",
"protein_id": "ENSP00000616588.1",
"transcript_support_level": null,
"aa_start": 401,
"aa_end": null,
"aa_length": 544,
"cds_start": 1202,
"cds_end": null,
"cds_length": 1635,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000946529.1"
},
{
"aa_ref": "K",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RYK",
"gene_hgnc_id": 10481,
"hgvs_c": "c.1145A>G",
"hgvs_p": "p.Lys382Arg",
"transcript": "ENST00000946532.1",
"protein_id": "ENSP00000616591.1",
"transcript_support_level": null,
"aa_start": 382,
"aa_end": null,
"aa_length": 525,
"cds_start": 1145,
"cds_end": null,
"cds_length": 1578,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000946532.1"
},
{
"aa_ref": "K",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RYK",
"gene_hgnc_id": 10481,
"hgvs_c": "c.1091A>G",
"hgvs_p": "p.Lys364Arg",
"transcript": "ENST00000946540.1",
"protein_id": "ENSP00000616599.1",
"transcript_support_level": null,
"aa_start": 364,
"aa_end": null,
"aa_length": 507,
"cds_start": 1091,
"cds_end": null,
"cds_length": 1524,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000946540.1"
},
{
"aa_ref": "K",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RYK",
"gene_hgnc_id": 10481,
"hgvs_c": "c.1019A>G",
"hgvs_p": "p.Lys340Arg",
"transcript": "ENST00000946536.1",
"protein_id": "ENSP00000616595.1",
"transcript_support_level": null,
"aa_start": 340,
"aa_end": null,
"aa_length": 483,
"cds_start": 1019,
"cds_end": null,
"cds_length": 1452,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000946536.1"
},
{
"aa_ref": "K",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RYK",
"gene_hgnc_id": 10481,
"hgvs_c": "c.965A>G",
"hgvs_p": "p.Lys322Arg",
"transcript": "ENST00000912306.1",
"protein_id": "ENSP00000582365.1",
"transcript_support_level": null,
"aa_start": 322,
"aa_end": null,
"aa_length": 465,
"cds_start": 965,
"cds_end": null,
"cds_length": 1398,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000912306.1"
},
{
"aa_ref": "K",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RYK",
"gene_hgnc_id": 10481,
"hgvs_c": "c.956A>G",
"hgvs_p": "p.Lys319Arg",
"transcript": "ENST00000946531.1",
"protein_id": "ENSP00000616590.1",
"transcript_support_level": null,
"aa_start": 319,
"aa_end": null,
"aa_length": 462,
"cds_start": 956,
"cds_end": null,
"cds_length": 1389,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000946531.1"
},
{
"aa_ref": "K",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RYK",
"gene_hgnc_id": 10481,
"hgvs_c": "c.932A>G",
"hgvs_p": "p.Lys311Arg",
"transcript": "ENST00000946537.1",
"protein_id": "ENSP00000616596.1",
"transcript_support_level": null,
"aa_start": 311,
"aa_end": null,
"aa_length": 454,
"cds_start": 932,
"cds_end": null,
"cds_length": 1365,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000946537.1"
},
{
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{
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{
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{
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{
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{
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],
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{
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"non_coding_transcript_exon_variant"
],
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"gene_symbol": "RYK",
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"biotype": "pseudogene",
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},
{
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"3_prime_UTR_variant"
],
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"gene_symbol": "RYK",
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"feature": "ENST00000486725.1"
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],
"gene_symbol": "RYK",
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"dbsnp": "rs116254638",
"frequency_reference_population": 0.0011615506,
"hom_count_reference_population": 30,
"allele_count_reference_population": 1869,
"gnomad_exomes_af": 0.000640471,
"gnomad_genomes_af": 0.00614512,
"gnomad_exomes_ac": 933,
"gnomad_genomes_ac": 936,
"gnomad_exomes_homalt": 19,
"gnomad_genomes_homalt": 11,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.012388795614242554,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.573,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": 0.1016,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.29,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 5.886,
"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": -20,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6_Very_Strong,BS1,BS2",
"acmg_by_gene": [
{
"score": -20,
"benign_score": 20,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong",
"BS1",
"BS2"
],
"verdict": "Benign",
"transcript": "NM_001005861.3",
"gene_symbol": "RYK",
"hgnc_id": 10481,
"effects": [
"missense_variant"
],
"inheritance_mode": "AD",
"hgvs_c": "c.1400A>G",
"hgvs_p": "p.Lys467Arg"
}
],
"clinvar_disease": "not provided",
"clinvar_classification": "Benign",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "B:2",
"phenotype_combined": "not provided",
"pathogenicity_classification_combined": "Benign",
"custom_annotations": null
}
],
"message": null
}