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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: 7-107917307-A-G (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=7&pos=107917307&ref=A&alt=G&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "7",
"pos": 107917307,
"ref": "A",
"alt": "G",
"effect": "missense_variant",
"transcript": "NM_000108.5",
"consequences": [
{
"aa_ref": "M",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DLD",
"gene_hgnc_id": 2898,
"hgvs_c": "c.1081A>G",
"hgvs_p": "p.Met361Val",
"transcript": "NM_000108.5",
"protein_id": "NP_000099.2",
"transcript_support_level": null,
"aa_start": 361,
"aa_end": null,
"aa_length": 509,
"cds_start": 1081,
"cds_end": null,
"cds_length": 1530,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000205402.10",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_000108.5"
},
{
"aa_ref": "M",
"aa_alt": "V",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DLD",
"gene_hgnc_id": 2898,
"hgvs_c": "c.1081A>G",
"hgvs_p": "p.Met361Val",
"transcript": "ENST00000205402.10",
"protein_id": "ENSP00000205402.3",
"transcript_support_level": 1,
"aa_start": 361,
"aa_end": null,
"aa_length": 509,
"cds_start": 1081,
"cds_end": null,
"cds_length": 1530,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_000108.5",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000205402.10"
},
{
"aa_ref": "M",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DLD",
"gene_hgnc_id": 2898,
"hgvs_c": "c.1063A>G",
"hgvs_p": "p.Met355Val",
"transcript": "ENST00000880448.1",
"protein_id": "ENSP00000550507.1",
"transcript_support_level": null,
"aa_start": 355,
"aa_end": null,
"aa_length": 503,
"cds_start": 1063,
"cds_end": null,
"cds_length": 1512,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000880448.1"
},
{
"aa_ref": "M",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DLD",
"gene_hgnc_id": 2898,
"hgvs_c": "c.1057A>G",
"hgvs_p": "p.Met353Val",
"transcript": "ENST00000880447.1",
"protein_id": "ENSP00000550506.1",
"transcript_support_level": null,
"aa_start": 353,
"aa_end": null,
"aa_length": 501,
"cds_start": 1057,
"cds_end": null,
"cds_length": 1506,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000880447.1"
},
{
"aa_ref": "M",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DLD",
"gene_hgnc_id": 2898,
"hgvs_c": "c.1045A>G",
"hgvs_p": "p.Met349Val",
"transcript": "ENST00000880450.1",
"protein_id": "ENSP00000550509.1",
"transcript_support_level": null,
"aa_start": 349,
"aa_end": null,
"aa_length": 497,
"cds_start": 1045,
"cds_end": null,
"cds_length": 1494,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000880450.1"
},
{
"aa_ref": "M",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DLD",
"gene_hgnc_id": 2898,
"hgvs_c": "c.1015A>G",
"hgvs_p": "p.Met339Val",
"transcript": "ENST00000924909.1",
"protein_id": "ENSP00000594968.1",
"transcript_support_level": null,
"aa_start": 339,
"aa_end": null,
"aa_length": 487,
"cds_start": 1015,
"cds_end": null,
"cds_length": 1464,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000924909.1"
},
{
"aa_ref": "M",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DLD",
"gene_hgnc_id": 2898,
"hgvs_c": "c.1012A>G",
"hgvs_p": "p.Met338Val",
"transcript": "NM_001289751.1",
"protein_id": "NP_001276680.1",
"transcript_support_level": null,
"aa_start": 338,
"aa_end": null,
"aa_length": 486,
"cds_start": 1012,
"cds_end": null,
"cds_length": 1461,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001289751.1"
},
{
"aa_ref": "M",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DLD",
"gene_hgnc_id": 2898,
"hgvs_c": "c.1012A>G",
"hgvs_p": "p.Met338Val",
"transcript": "ENST00000440410.5",
"protein_id": "ENSP00000417016.1",
"transcript_support_level": 2,
"aa_start": 338,
"aa_end": null,
"aa_length": 486,
"cds_start": 1012,
"cds_end": null,
"cds_length": 1461,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000440410.5"
},
{
"aa_ref": "M",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DLD",
"gene_hgnc_id": 2898,
"hgvs_c": "c.994A>G",
"hgvs_p": "p.Met332Val",
"transcript": "ENST00000880449.1",
"protein_id": "ENSP00000550508.1",
"transcript_support_level": null,
"aa_start": 332,
"aa_end": null,
"aa_length": 480,
"cds_start": 994,
"cds_end": null,
"cds_length": 1443,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000880449.1"
},
{
"aa_ref": "M",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DLD",
"gene_hgnc_id": 2898,
"hgvs_c": "c.1081A>G",
"hgvs_p": "p.Met361Val",
"transcript": "ENST00000880451.1",
"protein_id": "ENSP00000550510.1",
"transcript_support_level": null,
"aa_start": 361,
"aa_end": null,
"aa_length": 479,
"cds_start": 1081,
"cds_end": null,
"cds_length": 1440,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000880451.1"
},
{
"aa_ref": "M",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DLD",
"gene_hgnc_id": 2898,
"hgvs_c": "c.961A>G",
"hgvs_p": "p.Met321Val",
"transcript": "ENST00000880452.1",
"protein_id": "ENSP00000550511.1",
"transcript_support_level": null,
"aa_start": 321,
"aa_end": null,
"aa_length": 469,
"cds_start": 961,
"cds_end": null,
"cds_length": 1410,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000880452.1"
},
{
"aa_ref": "M",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DLD",
"gene_hgnc_id": 2898,
"hgvs_c": "c.937A>G",
"hgvs_p": "p.Met313Val",
"transcript": "NM_001289752.1",
"protein_id": "NP_001276681.1",
"transcript_support_level": null,
"aa_start": 313,
"aa_end": null,
"aa_length": 461,
"cds_start": 937,
"cds_end": null,
"cds_length": 1386,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001289752.1"
},
{
"aa_ref": "M",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DLD",
"gene_hgnc_id": 2898,
"hgvs_c": "c.937A>G",
"hgvs_p": "p.Met313Val",
"transcript": "ENST00000437604.6",
"protein_id": "ENSP00000387542.2",
"transcript_support_level": 2,
"aa_start": 313,
"aa_end": null,
"aa_length": 461,
"cds_start": 937,
"cds_end": null,
"cds_length": 1386,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000437604.6"
},
{
"aa_ref": "M",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DLD",
"gene_hgnc_id": 2898,
"hgvs_c": "c.910A>G",
"hgvs_p": "p.Met304Val",
"transcript": "ENST00000924908.1",
"protein_id": "ENSP00000594967.1",
"transcript_support_level": null,
"aa_start": 304,
"aa_end": null,
"aa_length": 452,
"cds_start": 910,
"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": "ENST00000924908.1"
},
{
"aa_ref": "M",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DLD",
"gene_hgnc_id": 2898,
"hgvs_c": "c.853A>G",
"hgvs_p": "p.Met285Val",
"transcript": "ENST00000957323.1",
"protein_id": "ENSP00000627382.1",
"transcript_support_level": null,
"aa_start": 285,
"aa_end": null,
"aa_length": 433,
"cds_start": 853,
"cds_end": null,
"cds_length": 1302,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000957323.1"
},
{
"aa_ref": "M",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DLD",
"gene_hgnc_id": 2898,
"hgvs_c": "c.835A>G",
"hgvs_p": "p.Met279Val",
"transcript": "ENST00000924910.1",
"protein_id": "ENSP00000594969.1",
"transcript_support_level": null,
"aa_start": 279,
"aa_end": null,
"aa_length": 427,
"cds_start": 835,
"cds_end": null,
"cds_length": 1284,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000924910.1"
},
{
"aa_ref": "M",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DLD",
"gene_hgnc_id": 2898,
"hgvs_c": "c.784A>G",
"hgvs_p": "p.Met262Val",
"transcript": "NM_001289750.1",
"protein_id": "NP_001276679.1",
"transcript_support_level": null,
"aa_start": 262,
"aa_end": null,
"aa_length": 410,
"cds_start": 784,
"cds_end": null,
"cds_length": 1233,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001289750.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DLD",
"gene_hgnc_id": 2898,
"hgvs_c": "n.*755A>G",
"hgvs_p": null,
"transcript": "ENST00000415325.5",
"protein_id": "ENSP00000402593.1",
"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": "nonsense_mediated_decay",
"feature": "ENST00000415325.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DLD",
"gene_hgnc_id": 2898,
"hgvs_c": "n.1081A>G",
"hgvs_p": null,
"transcript": "ENST00000417551.5",
"protein_id": "ENSP00000390667.1",
"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": "ENST00000417551.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DLD",
"gene_hgnc_id": 2898,
"hgvs_c": "n.*755A>G",
"hgvs_p": null,
"transcript": "ENST00000415325.5",
"protein_id": "ENSP00000402593.1",
"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": "nonsense_mediated_decay",
"feature": "ENST00000415325.5"
}
],
"gene_symbol": "DLD",
"gene_hgnc_id": 2898,
"dbsnp": "rs121964993",
"frequency_reference_population": 0.000015733747,
"hom_count_reference_population": 0,
"allele_count_reference_population": 23,
"gnomad_exomes_af": 0.0000157337,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": 23,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.9453363418579102,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.009999999776482582,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.795,
"revel_prediction": "Pathogenic",
"alphamissense_score": 0.7791,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.36,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 9.325,
"phylop100way_prediction": "Pathogenic",
"spliceai_max_score": 0.01,
"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": 14,
"acmg_classification": "Pathogenic",
"acmg_criteria": "PM2,PP3_Strong,PP5_Very_Strong",
"acmg_by_gene": [
{
"score": 14,
"benign_score": 0,
"pathogenic_score": 14,
"criteria": [
"PM2",
"PP3_Strong",
"PP5_Very_Strong"
],
"verdict": "Pathogenic",
"transcript": "NM_000108.5",
"gene_symbol": "DLD",
"hgnc_id": 2898,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.1081A>G",
"hgvs_p": "p.Met361Val"
}
],
"clinvar_disease": "Pyruvate dehydrogenase E3 deficiency",
"clinvar_classification": "Likely pathogenic",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "LP:4",
"phenotype_combined": "Pyruvate dehydrogenase E3 deficiency",
"pathogenicity_classification_combined": "Likely pathogenic",
"custom_annotations": null
}
],
"message": null
}