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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: 19-422187-C-G (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=19&pos=422187&ref=C&alt=G&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "19",
"pos": 422187,
"ref": "C",
"alt": "G",
"effect": "missense_variant",
"transcript": "NM_012435.3",
"consequences": [
{
"aa_ref": "G",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SHC2",
"gene_hgnc_id": 29869,
"hgvs_c": "c.1579G>C",
"hgvs_p": "p.Gly527Arg",
"transcript": "NM_012435.3",
"protein_id": "NP_036567.2",
"transcript_support_level": null,
"aa_start": 527,
"aa_end": null,
"aa_length": 582,
"cds_start": 1579,
"cds_end": null,
"cds_length": 1749,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000264554.11",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_012435.3"
},
{
"aa_ref": "G",
"aa_alt": "R",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SHC2",
"gene_hgnc_id": 29869,
"hgvs_c": "c.1579G>C",
"hgvs_p": "p.Gly527Arg",
"transcript": "ENST00000264554.11",
"protein_id": "ENSP00000264554.4",
"transcript_support_level": 1,
"aa_start": 527,
"aa_end": null,
"aa_length": 582,
"cds_start": 1579,
"cds_end": null,
"cds_length": 1749,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_012435.3",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000264554.11"
},
{
"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": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SHC2",
"gene_hgnc_id": 29869,
"hgvs_c": "n.642G>C",
"hgvs_p": null,
"transcript": "ENST00000588376.5",
"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": "ENST00000588376.5"
},
{
"aa_ref": "G",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SHC2",
"gene_hgnc_id": 29869,
"hgvs_c": "c.1657G>C",
"hgvs_p": "p.Gly553Arg",
"transcript": "ENST00000945174.1",
"protein_id": "ENSP00000615233.1",
"transcript_support_level": null,
"aa_start": 553,
"aa_end": null,
"aa_length": 608,
"cds_start": 1657,
"cds_end": null,
"cds_length": 1827,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000945174.1"
},
{
"aa_ref": "G",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SHC2",
"gene_hgnc_id": 29869,
"hgvs_c": "c.1654G>C",
"hgvs_p": "p.Gly552Arg",
"transcript": "ENST00000945166.1",
"protein_id": "ENSP00000615225.1",
"transcript_support_level": null,
"aa_start": 552,
"aa_end": null,
"aa_length": 607,
"cds_start": 1654,
"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": "ENST00000945166.1"
},
{
"aa_ref": "G",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SHC2",
"gene_hgnc_id": 29869,
"hgvs_c": "c.1627G>C",
"hgvs_p": "p.Gly543Arg",
"transcript": "ENST00000945164.1",
"protein_id": "ENSP00000615223.1",
"transcript_support_level": null,
"aa_start": 543,
"aa_end": null,
"aa_length": 598,
"cds_start": 1627,
"cds_end": null,
"cds_length": 1797,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000945164.1"
},
{
"aa_ref": "G",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SHC2",
"gene_hgnc_id": 29869,
"hgvs_c": "c.1606G>C",
"hgvs_p": "p.Gly536Arg",
"transcript": "ENST00000945167.1",
"protein_id": "ENSP00000615226.1",
"transcript_support_level": null,
"aa_start": 536,
"aa_end": null,
"aa_length": 591,
"cds_start": 1606,
"cds_end": null,
"cds_length": 1776,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000945167.1"
},
{
"aa_ref": "G",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SHC2",
"gene_hgnc_id": 29869,
"hgvs_c": "c.1579G>C",
"hgvs_p": "p.Gly527Arg",
"transcript": "ENST00000945169.1",
"protein_id": "ENSP00000615228.1",
"transcript_support_level": null,
"aa_start": 527,
"aa_end": null,
"aa_length": 582,
"cds_start": 1579,
"cds_end": null,
"cds_length": 1749,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000945169.1"
},
{
"aa_ref": "G",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SHC2",
"gene_hgnc_id": 29869,
"hgvs_c": "c.1579G>C",
"hgvs_p": "p.Gly527Arg",
"transcript": "ENST00000945175.1",
"protein_id": "ENSP00000615234.1",
"transcript_support_level": null,
"aa_start": 527,
"aa_end": null,
"aa_length": 582,
"cds_start": 1579,
"cds_end": null,
"cds_length": 1749,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000945175.1"
},
{
"aa_ref": "G",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SHC2",
"gene_hgnc_id": 29869,
"hgvs_c": "c.1579G>C",
"hgvs_p": "p.Gly527Arg",
"transcript": "ENST00000945172.1",
"protein_id": "ENSP00000615231.1",
"transcript_support_level": null,
"aa_start": 527,
"aa_end": null,
"aa_length": 581,
"cds_start": 1579,
"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": "ENST00000945172.1"
},
{
"aa_ref": "G",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SHC2",
"gene_hgnc_id": 29869,
"hgvs_c": "c.1546G>C",
"hgvs_p": "p.Gly516Arg",
"transcript": "ENST00000945165.1",
"protein_id": "ENSP00000615224.1",
"transcript_support_level": null,
"aa_start": 516,
"aa_end": null,
"aa_length": 571,
"cds_start": 1546,
"cds_end": null,
"cds_length": 1716,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000945165.1"
},
{
"aa_ref": "G",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SHC2",
"gene_hgnc_id": 29869,
"hgvs_c": "c.1525G>C",
"hgvs_p": "p.Gly509Arg",
"transcript": "ENST00000945171.1",
"protein_id": "ENSP00000615230.1",
"transcript_support_level": null,
"aa_start": 509,
"aa_end": null,
"aa_length": 564,
"cds_start": 1525,
"cds_end": null,
"cds_length": 1695,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000945171.1"
},
{
"aa_ref": "G",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SHC2",
"gene_hgnc_id": 29869,
"hgvs_c": "c.1519G>C",
"hgvs_p": "p.Gly507Arg",
"transcript": "ENST00000945170.1",
"protein_id": "ENSP00000615229.1",
"transcript_support_level": null,
"aa_start": 507,
"aa_end": null,
"aa_length": 562,
"cds_start": 1519,
"cds_end": null,
"cds_length": 1689,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000945170.1"
},
{
"aa_ref": "G",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SHC2",
"gene_hgnc_id": 29869,
"hgvs_c": "c.1444G>C",
"hgvs_p": "p.Gly482Arg",
"transcript": "NM_001387056.1",
"protein_id": "NP_001373985.1",
"transcript_support_level": null,
"aa_start": 482,
"aa_end": null,
"aa_length": 537,
"cds_start": 1444,
"cds_end": null,
"cds_length": 1614,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001387056.1"
},
{
"aa_ref": "G",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SHC2",
"gene_hgnc_id": 29869,
"hgvs_c": "c.1444G>C",
"hgvs_p": "p.Gly482Arg",
"transcript": "ENST00000939515.1",
"protein_id": "ENSP00000609574.1",
"transcript_support_level": null,
"aa_start": 482,
"aa_end": null,
"aa_length": 537,
"cds_start": 1444,
"cds_end": null,
"cds_length": 1614,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000939515.1"
},
{
"aa_ref": "G",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SHC2",
"gene_hgnc_id": 29869,
"hgvs_c": "c.1189G>C",
"hgvs_p": "p.Gly397Arg",
"transcript": "ENST00000945168.1",
"protein_id": "ENSP00000615227.1",
"transcript_support_level": null,
"aa_start": 397,
"aa_end": null,
"aa_length": 452,
"cds_start": 1189,
"cds_end": null,
"cds_length": 1359,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000945168.1"
},
{
"aa_ref": "G",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SHC2",
"gene_hgnc_id": 29869,
"hgvs_c": "c.1042G>C",
"hgvs_p": "p.Gly348Arg",
"transcript": "ENST00000945173.1",
"protein_id": "ENSP00000615232.1",
"transcript_support_level": null,
"aa_start": 348,
"aa_end": null,
"aa_length": 403,
"cds_start": 1042,
"cds_end": null,
"cds_length": 1212,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000945173.1"
},
{
"aa_ref": "G",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SHC2",
"gene_hgnc_id": 29869,
"hgvs_c": "c.1579G>C",
"hgvs_p": "p.Gly527Arg",
"transcript": "XM_011527893.4",
"protein_id": "XP_011526195.1",
"transcript_support_level": null,
"aa_start": 527,
"aa_end": null,
"aa_length": 594,
"cds_start": 1579,
"cds_end": null,
"cds_length": 1785,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_011527893.4"
},
{
"aa_ref": "G",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SHC2",
"gene_hgnc_id": 29869,
"hgvs_c": "c.1444G>C",
"hgvs_p": "p.Gly482Arg",
"transcript": "XM_011527894.3",
"protein_id": "XP_011526196.1",
"transcript_support_level": null,
"aa_start": 482,
"aa_end": null,
"aa_length": 549,
"cds_start": 1444,
"cds_end": null,
"cds_length": 1650,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_011527894.3"
},
{
"aa_ref": "G",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SHC2",
"gene_hgnc_id": 29869,
"hgvs_c": "c.1108G>C",
"hgvs_p": "p.Gly370Arg",
"transcript": "XM_011527896.3",
"protein_id": "XP_011526198.1",
"transcript_support_level": null,
"aa_start": 370,
"aa_end": null,
"aa_length": 437,
"cds_start": 1108,
"cds_end": null,
"cds_length": 1314,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_011527896.3"
},
{
"aa_ref": "G",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SHC2",
"gene_hgnc_id": 29869,
"hgvs_c": "c.1108G>C",
"hgvs_p": "p.Gly370Arg",
"transcript": "XM_047438565.1",
"protein_id": "XP_047294521.1",
"transcript_support_level": null,
"aa_start": 370,
"aa_end": null,
"aa_length": 437,
"cds_start": 1108,
"cds_end": null,
"cds_length": 1314,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047438565.1"
},
{
"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": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SHC2",
"gene_hgnc_id": 29869,
"hgvs_c": "n.*102G>C",
"hgvs_p": null,
"transcript": "ENST00000590170.3",
"protein_id": "ENSP00000465764.3",
"transcript_support_level": 5,
"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": "ENST00000590170.3"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SHC2",
"gene_hgnc_id": 29869,
"hgvs_c": "n.*102G>C",
"hgvs_p": null,
"transcript": "ENST00000590170.3",
"protein_id": "ENSP00000465764.3",
"transcript_support_level": 5,
"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": "ENST00000590170.3"
}
],
"gene_symbol": "SHC2",
"gene_hgnc_id": 29869,
"dbsnp": "rs779103557",
"frequency_reference_population": null,
"hom_count_reference_population": 0,
"allele_count_reference_population": 0,
"gnomad_exomes_af": null,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": null,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": null,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.9154037237167358,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.703,
"revel_prediction": "Pathogenic",
"alphamissense_score": 0.5355,
"alphamissense_prediction": "Uncertain_significance",
"bayesdelnoaf_score": 0.26,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 5.623,
"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": "Uncertain_significance",
"acmg_criteria": "PM2,PP3_Moderate",
"acmg_by_gene": [
{
"score": 4,
"benign_score": 0,
"pathogenic_score": 4,
"criteria": [
"PM2",
"PP3_Moderate"
],
"verdict": "Uncertain_significance",
"transcript": "NM_012435.3",
"gene_symbol": "SHC2",
"hgnc_id": 29869,
"effects": [
"missense_variant"
],
"inheritance_mode": "",
"hgvs_c": "c.1579G>C",
"hgvs_p": "p.Gly527Arg"
}
],
"clinvar_disease": "",
"clinvar_classification": "",
"clinvar_review_status": "",
"clinvar_submissions_summary": "",
"phenotype_combined": null,
"pathogenicity_classification_combined": null,
"custom_annotations": null
}
],
"message": null
}