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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: 12-57232799-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=12&pos=57232799&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 11,
"criteria": [
"BP4_Moderate",
"BP7",
"BA1"
],
"effects": [
"synonymous_variant"
],
"gene_symbol": "SHMT2",
"hgnc_id": 10852,
"hgvs_c": "c.813G>A",
"hgvs_p": "p.Ala271Ala",
"inheritance_mode": "AR",
"pathogenic_score": 0,
"score": -11,
"transcript": "NM_005412.6",
"verdict": "Benign"
}
],
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Moderate,BP7,BA1",
"acmg_score": -11,
"allele_count_reference_population": 58216,
"alphamissense_prediction": null,
"alphamissense_score": null,
"alt": "A",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Benign",
"bayesdelnoaf_score": -0.64,
"chr": "12",
"clinvar_classification": "",
"clinvar_disease": "",
"clinvar_review_status": "",
"clinvar_submissions_summary": "",
"computational_prediction_selected": "Benign",
"computational_score_selected": 0.08399999886751175,
"computational_source_selected": "REVEL",
"consequences": [
{
"aa_alt": "A",
"aa_end": null,
"aa_length": 504,
"aa_ref": "A",
"aa_start": 271,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2157,
"cdna_start": 881,
"cds_end": null,
"cds_length": 1515,
"cds_start": 813,
"consequences": [
"synonymous_variant"
],
"exon_count": 12,
"exon_rank": 7,
"exon_rank_end": null,
"feature": "NM_005412.6",
"gene_hgnc_id": 10852,
"gene_symbol": "SHMT2",
"hgvs_c": "c.813G>A",
"hgvs_p": "p.Ala271Ala",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000328923.8",
"protein_coding": true,
"protein_id": "NP_005403.2",
"strand": true,
"transcript": "NM_005412.6",
"transcript_support_level": null
},
{
"aa_alt": "A",
"aa_end": null,
"aa_length": 504,
"aa_ref": "A",
"aa_start": 271,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 2157,
"cdna_start": 881,
"cds_end": null,
"cds_length": 1515,
"cds_start": 813,
"consequences": [
"synonymous_variant"
],
"exon_count": 12,
"exon_rank": 7,
"exon_rank_end": null,
"feature": "ENST00000328923.8",
"gene_hgnc_id": 10852,
"gene_symbol": "SHMT2",
"hgvs_c": "c.813G>A",
"hgvs_p": "p.Ala271Ala",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_005412.6",
"protein_coding": true,
"protein_id": "ENSP00000333667.3",
"strand": true,
"transcript": "ENST00000328923.8",
"transcript_support_level": 1
},
{
"aa_alt": "A",
"aa_end": null,
"aa_length": 494,
"aa_ref": "A",
"aa_start": 261,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1918,
"cdna_start": 851,
"cds_end": null,
"cds_length": 1485,
"cds_start": 783,
"consequences": [
"synonymous_variant"
],
"exon_count": 12,
"exon_rank": 7,
"exon_rank_end": null,
"feature": "ENST00000557487.5",
"gene_hgnc_id": 10852,
"gene_symbol": "SHMT2",
"hgvs_c": "c.783G>A",
"hgvs_p": "p.Ala261Ala",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000452315.1",
"strand": true,
"transcript": "ENST00000557487.5",
"transcript_support_level": 1
},
{
"aa_alt": "A",
"aa_end": null,
"aa_length": 483,
"aa_ref": "A",
"aa_start": 250,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2006,
"cdna_start": 939,
"cds_end": null,
"cds_length": 1452,
"cds_start": 750,
"consequences": [
"synonymous_variant"
],
"exon_count": 12,
"exon_rank": 7,
"exon_rank_end": null,
"feature": "ENST00000414700.7",
"gene_hgnc_id": 10852,
"gene_symbol": "SHMT2",
"hgvs_c": "c.750G>A",
"hgvs_p": "p.Ala250Ala",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000406881.3",
"strand": true,
"transcript": "ENST00000414700.7",
"transcript_support_level": 1
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "nonsense_mediated_decay",
"canonical": false,
"cdna_end": null,
"cdna_length": 2311,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 11,
"exon_rank": 6,
"exon_rank_end": null,
"feature": "ENST00000555774.5",
"gene_hgnc_id": 10852,
"gene_symbol": "SHMT2",
"hgvs_c": "n.*500G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000451872.1",
"strand": true,
"transcript": "ENST00000555774.5",
"transcript_support_level": 1
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "nonsense_mediated_decay",
"canonical": false,
"cdna_end": null,
"cdna_length": 2215,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 11,
"exon_rank": 6,
"exon_rank_end": null,
"feature": "ENST00000556825.5",
"gene_hgnc_id": 10852,
"gene_symbol": "SHMT2",
"hgvs_c": "n.*472G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000451169.1",
"strand": true,
"transcript": "ENST00000556825.5",
"transcript_support_level": 1
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "nonsense_mediated_decay",
"canonical": false,
"cdna_end": null,
"cdna_length": 1904,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 12,
"exon_rank": 7,
"exon_rank_end": null,
"feature": "ENST00000557433.5",
"gene_hgnc_id": 10852,
"gene_symbol": "SHMT2",
"hgvs_c": "n.*301G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000450610.1",
"strand": true,
"transcript": "ENST00000557433.5",
"transcript_support_level": 1
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "nonsense_mediated_decay",
"canonical": false,
"cdna_end": null,
"cdna_length": 2311,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"3_prime_UTR_variant"
],
"exon_count": 11,
"exon_rank": 6,
"exon_rank_end": null,
"feature": "ENST00000555774.5",
"gene_hgnc_id": 10852,
"gene_symbol": "SHMT2",
"hgvs_c": "n.*500G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000451872.1",
"strand": true,
"transcript": "ENST00000555774.5",
"transcript_support_level": 1
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "nonsense_mediated_decay",
"canonical": false,
"cdna_end": null,
"cdna_length": 2215,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"3_prime_UTR_variant"
],
"exon_count": 11,
"exon_rank": 6,
"exon_rank_end": null,
"feature": "ENST00000556825.5",
"gene_hgnc_id": 10852,
"gene_symbol": "SHMT2",
"hgvs_c": "n.*472G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000451169.1",
"strand": true,
"transcript": "ENST00000556825.5",
"transcript_support_level": 1
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "nonsense_mediated_decay",
"canonical": false,
"cdna_end": null,
"cdna_length": 1904,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"3_prime_UTR_variant"
],
"exon_count": 12,
"exon_rank": 7,
"exon_rank_end": null,
"feature": "ENST00000557433.5",
"gene_hgnc_id": 10852,
"gene_symbol": "SHMT2",
"hgvs_c": "n.*301G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000450610.1",
"strand": true,
"transcript": "ENST00000557433.5",
"transcript_support_level": 1
},
{
"aa_alt": "A",
"aa_end": null,
"aa_length": 545,
"aa_ref": "A",
"aa_start": 271,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2070,
"cdna_start": 880,
"cds_end": null,
"cds_length": 1638,
"cds_start": 813,
"consequences": [
"synonymous_variant"
],
"exon_count": 12,
"exon_rank": 7,
"exon_rank_end": null,
"feature": "ENST00000894753.1",
"gene_hgnc_id": 10852,
"gene_symbol": "SHMT2",
"hgvs_c": "c.813G>A",
"hgvs_p": "p.Ala271Ala",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000564812.1",
"strand": true,
"transcript": "ENST00000894753.1",
"transcript_support_level": null
},
{
"aa_alt": "A",
"aa_end": null,
"aa_length": 513,
"aa_ref": "A",
"aa_start": 280,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1973,
"cdna_start": 908,
"cds_end": null,
"cds_length": 1542,
"cds_start": 840,
"consequences": [
"synonymous_variant"
],
"exon_count": 12,
"exon_rank": 7,
"exon_rank_end": null,
"feature": "ENST00000894754.1",
"gene_hgnc_id": 10852,
"gene_symbol": "SHMT2",
"hgvs_c": "c.840G>A",
"hgvs_p": "p.Ala280Ala",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000564813.1",
"strand": true,
"transcript": "ENST00000894754.1",
"transcript_support_level": null
},
{
"aa_alt": "A",
"aa_end": null,
"aa_length": 509,
"aa_ref": "A",
"aa_start": 271,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2007,
"cdna_start": 925,
"cds_end": null,
"cds_length": 1530,
"cds_start": 813,
"consequences": [
"synonymous_variant"
],
"exon_count": 12,
"exon_rank": 7,
"exon_rank_end": null,
"feature": "ENST00000894751.1",
"gene_hgnc_id": 10852,
"gene_symbol": "SHMT2",
"hgvs_c": "c.813G>A",
"hgvs_p": "p.Ala271Ala",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000564810.1",
"strand": true,
"transcript": "ENST00000894751.1",
"transcript_support_level": null
},
{
"aa_alt": "A",
"aa_end": null,
"aa_length": 504,
"aa_ref": "A",
"aa_start": 271,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2080,
"cdna_start": 1013,
"cds_end": null,
"cds_length": 1515,
"cds_start": 813,
"consequences": [
"synonymous_variant"
],
"exon_count": 14,
"exon_rank": 9,
"exon_rank_end": null,
"feature": "ENST00000925589.1",
"gene_hgnc_id": 10852,
"gene_symbol": "SHMT2",
"hgvs_c": "c.813G>A",
"hgvs_p": "p.Ala271Ala",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000595648.1",
"strand": true,
"transcript": "ENST00000925589.1",
"transcript_support_level": null
},
{
"aa_alt": "A",
"aa_end": null,
"aa_length": 504,
"aa_ref": "A",
"aa_start": 271,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2120,
"cdna_start": 1055,
"cds_end": null,
"cds_length": 1515,
"cds_start": 813,
"consequences": [
"synonymous_variant"
],
"exon_count": 14,
"exon_rank": 9,
"exon_rank_end": null,
"feature": "ENST00000925590.1",
"gene_hgnc_id": 10852,
"gene_symbol": "SHMT2",
"hgvs_c": "c.813G>A",
"hgvs_p": "p.Ala271Ala",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000595649.1",
"strand": true,
"transcript": "ENST00000925590.1",
"transcript_support_level": null
},
{
"aa_alt": "A",
"aa_end": null,
"aa_length": 504,
"aa_ref": "A",
"aa_start": 271,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2086,
"cdna_start": 1019,
"cds_end": null,
"cds_length": 1515,
"cds_start": 813,
"consequences": [
"synonymous_variant"
],
"exon_count": 14,
"exon_rank": 9,
"exon_rank_end": null,
"feature": "ENST00000925591.1",
"gene_hgnc_id": 10852,
"gene_symbol": "SHMT2",
"hgvs_c": "c.813G>A",
"hgvs_p": "p.Ala271Ala",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000595650.1",
"strand": true,
"transcript": "ENST00000925591.1",
"transcript_support_level": null
},
{
"aa_alt": "A",
"aa_end": null,
"aa_length": 496,
"aa_ref": "A",
"aa_start": 271,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1924,
"cdna_start": 881,
"cds_end": null,
"cds_length": 1491,
"cds_start": 813,
"consequences": [
"synonymous_variant"
],
"exon_count": 12,
"exon_rank": 7,
"exon_rank_end": null,
"feature": "ENST00000925592.1",
"gene_hgnc_id": 10852,
"gene_symbol": "SHMT2",
"hgvs_c": "c.813G>A",
"hgvs_p": "p.Ala271Ala",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000595651.1",
"strand": true,
"transcript": "ENST00000925592.1",
"transcript_support_level": null
},
{
"aa_alt": "A",
"aa_end": null,
"aa_length": 494,
"aa_ref": "A",
"aa_start": 261,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2127,
"cdna_start": 851,
"cds_end": null,
"cds_length": 1485,
"cds_start": 783,
"consequences": [
"synonymous_variant"
],
"exon_count": 12,
"exon_rank": 7,
"exon_rank_end": null,
"feature": "NM_001166356.2",
"gene_hgnc_id": 10852,
"gene_symbol": "SHMT2",
"hgvs_c": "c.783G>A",
"hgvs_p": "p.Ala261Ala",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001159828.1",
"strand": true,
"transcript": "NM_001166356.2",
"transcript_support_level": null
},
{
"aa_alt": "A",
"aa_end": null,
"aa_length": 492,
"aa_ref": "A",
"aa_start": 271,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1911,
"cdna_start": 881,
"cds_end": null,
"cds_length": 1479,
"cds_start": 813,
"consequences": [
"synonymous_variant"
],
"exon_count": 12,
"exon_rank": 7,
"exon_rank_end": null,
"feature": "ENST00000894752.1",
"gene_hgnc_id": 10852,
"gene_symbol": "SHMT2",
"hgvs_c": "c.813G>A",
"hgvs_p": "p.Ala271Ala",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000564811.1",
"strand": true,
"transcript": "ENST00000894752.1",
"transcript_support_level": null
},
{
"aa_alt": "A",
"aa_end": null,
"aa_length": 483,
"aa_ref": "A",
"aa_start": 250,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2357,
"cdna_start": 1081,
"cds_end": null,
"cds_length": 1452,
"cds_start": 750,
"consequences": [
"synonymous_variant"
],
"exon_count": 12,
"exon_rank": 7,
"exon_rank_end": null,
"feature": "NM_001166357.1",
"gene_hgnc_id": 10852,
"gene_symbol": "SHMT2",
"hgvs_c": "c.750G>A",
"hgvs_p": "p.Ala250Ala",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001159829.1",
"strand": true,
"transcript": "NM_001166357.1",
"transcript_support_level": null
},
{
"aa_alt": "A",
"aa_end": null,
"aa_length": 483,
"aa_ref": "A",
"aa_start": 250,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2159,
"cdna_start": 883,
"cds_end": null,
"cds_length": 1452,
"cds_start": 750,
"consequences": [
"synonymous_variant"
],
"exon_count": 12,
"exon_rank": 7,
"exon_rank_end": null,
"feature": "NM_001166358.2",
"gene_hgnc_id": 10852,
"gene_symbol": "SHMT2",
"hgvs_c": "c.750G>A",
"hgvs_p": "p.Ala250Ala",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
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