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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: 19-418975-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=19&pos=418975&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "19",
"pos": 418975,
"ref": "C",
"alt": "T",
"effect": "missense_variant",
"transcript": "NM_012435.3",
"consequences": [
{
"aa_ref": "A",
"aa_alt": "T",
"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.1702G>A",
"hgvs_p": "p.Ala568Thr",
"transcript": "NM_012435.3",
"protein_id": "NP_036567.2",
"transcript_support_level": null,
"aa_start": 568,
"aa_end": null,
"aa_length": 582,
"cds_start": 1702,
"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": "A",
"aa_alt": "T",
"canonical": true,
"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.1702G>A",
"hgvs_p": "p.Ala568Thr",
"transcript": "ENST00000264554.11",
"protein_id": "ENSP00000264554.4",
"transcript_support_level": 1,
"aa_start": 568,
"aa_end": null,
"aa_length": 582,
"cds_start": 1702,
"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": 2,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SHC2",
"gene_hgnc_id": 29869,
"hgvs_c": "n.765G>A",
"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": "A",
"aa_alt": "T",
"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.1780G>A",
"hgvs_p": "p.Ala594Thr",
"transcript": "ENST00000945174.1",
"protein_id": "ENSP00000615233.1",
"transcript_support_level": null,
"aa_start": 594,
"aa_end": null,
"aa_length": 608,
"cds_start": 1780,
"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": "A",
"aa_alt": "T",
"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.1777G>A",
"hgvs_p": "p.Ala593Thr",
"transcript": "ENST00000945166.1",
"protein_id": "ENSP00000615225.1",
"transcript_support_level": null,
"aa_start": 593,
"aa_end": null,
"aa_length": 607,
"cds_start": 1777,
"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": "A",
"aa_alt": "T",
"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.1750G>A",
"hgvs_p": "p.Ala584Thr",
"transcript": "ENST00000945164.1",
"protein_id": "ENSP00000615223.1",
"transcript_support_level": null,
"aa_start": 584,
"aa_end": null,
"aa_length": 598,
"cds_start": 1750,
"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": "A",
"aa_alt": "T",
"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.1729G>A",
"hgvs_p": "p.Ala577Thr",
"transcript": "ENST00000945167.1",
"protein_id": "ENSP00000615226.1",
"transcript_support_level": null,
"aa_start": 577,
"aa_end": null,
"aa_length": 591,
"cds_start": 1729,
"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": "A",
"aa_alt": "T",
"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.1702G>A",
"hgvs_p": "p.Ala568Thr",
"transcript": "ENST00000945169.1",
"protein_id": "ENSP00000615228.1",
"transcript_support_level": null,
"aa_start": 568,
"aa_end": null,
"aa_length": 582,
"cds_start": 1702,
"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": "A",
"aa_alt": "T",
"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": "SHC2",
"gene_hgnc_id": 29869,
"hgvs_c": "c.1702G>A",
"hgvs_p": "p.Ala568Thr",
"transcript": "ENST00000945175.1",
"protein_id": "ENSP00000615234.1",
"transcript_support_level": null,
"aa_start": 568,
"aa_end": null,
"aa_length": 582,
"cds_start": 1702,
"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": "A",
"aa_alt": "T",
"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.1699G>A",
"hgvs_p": "p.Ala567Thr",
"transcript": "ENST00000945172.1",
"protein_id": "ENSP00000615231.1",
"transcript_support_level": null,
"aa_start": 567,
"aa_end": null,
"aa_length": 581,
"cds_start": 1699,
"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": "A",
"aa_alt": "T",
"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.1669G>A",
"hgvs_p": "p.Ala557Thr",
"transcript": "ENST00000945165.1",
"protein_id": "ENSP00000615224.1",
"transcript_support_level": null,
"aa_start": 557,
"aa_end": null,
"aa_length": 571,
"cds_start": 1669,
"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": "A",
"aa_alt": "T",
"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.1648G>A",
"hgvs_p": "p.Ala550Thr",
"transcript": "ENST00000945171.1",
"protein_id": "ENSP00000615230.1",
"transcript_support_level": null,
"aa_start": 550,
"aa_end": null,
"aa_length": 564,
"cds_start": 1648,
"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": "A",
"aa_alt": "T",
"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.1642G>A",
"hgvs_p": "p.Ala548Thr",
"transcript": "ENST00000945170.1",
"protein_id": "ENSP00000615229.1",
"transcript_support_level": null,
"aa_start": 548,
"aa_end": null,
"aa_length": 562,
"cds_start": 1642,
"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": "A",
"aa_alt": "T",
"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.1567G>A",
"hgvs_p": "p.Ala523Thr",
"transcript": "NM_001387056.1",
"protein_id": "NP_001373985.1",
"transcript_support_level": null,
"aa_start": 523,
"aa_end": null,
"aa_length": 537,
"cds_start": 1567,
"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": "A",
"aa_alt": "T",
"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.1567G>A",
"hgvs_p": "p.Ala523Thr",
"transcript": "ENST00000939515.1",
"protein_id": "ENSP00000609574.1",
"transcript_support_level": null,
"aa_start": 523,
"aa_end": null,
"aa_length": 537,
"cds_start": 1567,
"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": "A",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SHC2",
"gene_hgnc_id": 29869,
"hgvs_c": "c.1312G>A",
"hgvs_p": "p.Ala438Thr",
"transcript": "ENST00000945168.1",
"protein_id": "ENSP00000615227.1",
"transcript_support_level": null,
"aa_start": 438,
"aa_end": null,
"aa_length": 452,
"cds_start": 1312,
"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": "A",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SHC2",
"gene_hgnc_id": 29869,
"hgvs_c": "c.1165G>A",
"hgvs_p": "p.Ala389Thr",
"transcript": "ENST00000945173.1",
"protein_id": "ENSP00000615232.1",
"transcript_support_level": null,
"aa_start": 389,
"aa_end": null,
"aa_length": 403,
"cds_start": 1165,
"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": 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": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SHC2",
"gene_hgnc_id": 29869,
"hgvs_c": "n.905G>A",
"hgvs_p": null,
"transcript": "ENST00000587423.5",
"protein_id": null,
"transcript_support_level": 2,
"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": "ENST00000587423.5"
},
{
"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": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SHC2",
"gene_hgnc_id": 29869,
"hgvs_c": "n.*225G>A",
"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": 5,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SHC2",
"gene_hgnc_id": 29869,
"hgvs_c": "n.*225G>A",
"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": "rs200038781",
"frequency_reference_population": 0.000029636954,
"hom_count_reference_population": 0,
"allele_count_reference_population": 47,
"gnomad_exomes_af": 0.0000251133,
"gnomad_genomes_af": 0.0000722012,
"gnomad_exomes_ac": 36,
"gnomad_genomes_ac": 11,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.686964750289917,
"computational_prediction_selected": "Uncertain_significance",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.10999999940395355,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.244,
"revel_prediction": "Benign",
"alphamissense_score": 0.6124,
"alphamissense_prediction": "Pathogenic",
"bayesdelnoaf_score": -0.15,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 7.307,
"phylop100way_prediction": "Uncertain_significance",
"spliceai_max_score": 0.11,
"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": 0,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "",
"acmg_by_gene": [
{
"score": 0,
"benign_score": 0,
"pathogenic_score": 0,
"criteria": [],
"verdict": "Uncertain_significance",
"transcript": "NM_012435.3",
"gene_symbol": "SHC2",
"hgnc_id": 29869,
"effects": [
"missense_variant"
],
"inheritance_mode": "",
"hgvs_c": "c.1702G>A",
"hgvs_p": "p.Ala568Thr"
}
],
"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
}