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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: 7-76063553-TG-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=7&pos=76063553&ref=TG&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "7",
"pos": 76063553,
"ref": "TG",
"alt": "T",
"effect": "frameshift_variant",
"transcript": "NM_005918.4",
"consequences": [
{
"aa_ref": "G",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"frameshift_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MDH2",
"gene_hgnc_id": 6971,
"hgvs_c": "c.596delG",
"hgvs_p": "p.Gly199fs",
"transcript": "NM_005918.4",
"protein_id": "NP_005909.2",
"transcript_support_level": null,
"aa_start": 199,
"aa_end": null,
"aa_length": 338,
"cds_start": 596,
"cds_end": null,
"cds_length": 1017,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000315758.10",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_005918.4"
},
{
"aa_ref": "G",
"aa_alt": null,
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"frameshift_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MDH2",
"gene_hgnc_id": 6971,
"hgvs_c": "c.596delG",
"hgvs_p": "p.Gly199fs",
"transcript": "ENST00000315758.10",
"protein_id": "ENSP00000327070.5",
"transcript_support_level": 1,
"aa_start": 199,
"aa_end": null,
"aa_length": 338,
"cds_start": 596,
"cds_end": null,
"cds_length": 1017,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_005918.4",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000315758.10"
},
{
"aa_ref": "G",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"frameshift_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MDH2",
"gene_hgnc_id": 6971,
"hgvs_c": "c.596delG",
"hgvs_p": "p.Gly199fs",
"transcript": "ENST00000971443.1",
"protein_id": "ENSP00000641502.1",
"transcript_support_level": null,
"aa_start": 199,
"aa_end": null,
"aa_length": 360,
"cds_start": 596,
"cds_end": null,
"cds_length": 1083,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000971443.1"
},
{
"aa_ref": "G",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"frameshift_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MDH2",
"gene_hgnc_id": 6971,
"hgvs_c": "c.596delG",
"hgvs_p": "p.Gly199fs",
"transcript": "ENST00000854579.1",
"protein_id": "ENSP00000524638.1",
"transcript_support_level": null,
"aa_start": 199,
"aa_end": null,
"aa_length": 336,
"cds_start": 596,
"cds_end": null,
"cds_length": 1011,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000854579.1"
},
{
"aa_ref": "G",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"frameshift_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MDH2",
"gene_hgnc_id": 6971,
"hgvs_c": "c.596delG",
"hgvs_p": "p.Gly199fs",
"transcript": "ENST00000930051.1",
"protein_id": "ENSP00000600110.1",
"transcript_support_level": null,
"aa_start": 199,
"aa_end": null,
"aa_length": 334,
"cds_start": 596,
"cds_end": null,
"cds_length": 1005,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000930051.1"
},
{
"aa_ref": "G",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"frameshift_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MDH2",
"gene_hgnc_id": 6971,
"hgvs_c": "c.596delG",
"hgvs_p": "p.Gly199fs",
"transcript": "ENST00000854580.1",
"protein_id": "ENSP00000524639.1",
"transcript_support_level": null,
"aa_start": 199,
"aa_end": null,
"aa_length": 329,
"cds_start": 596,
"cds_end": null,
"cds_length": 990,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000854580.1"
},
{
"aa_ref": "G",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"frameshift_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MDH2",
"gene_hgnc_id": 6971,
"hgvs_c": "c.470delG",
"hgvs_p": "p.Gly157fs",
"transcript": "NM_001282403.2",
"protein_id": "NP_001269332.1",
"transcript_support_level": null,
"aa_start": 157,
"aa_end": null,
"aa_length": 296,
"cds_start": 470,
"cds_end": null,
"cds_length": 891,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001282403.2"
},
{
"aa_ref": "G",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"frameshift_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MDH2",
"gene_hgnc_id": 6971,
"hgvs_c": "c.470delG",
"hgvs_p": "p.Gly157fs",
"transcript": "ENST00000432020.2",
"protein_id": "ENSP00000408649.2",
"transcript_support_level": 2,
"aa_start": 157,
"aa_end": null,
"aa_length": 296,
"cds_start": 470,
"cds_end": null,
"cds_length": 891,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000432020.2"
},
{
"aa_ref": "G",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"frameshift_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MDH2",
"gene_hgnc_id": 6971,
"hgvs_c": "c.314delG",
"hgvs_p": "p.Gly105fs",
"transcript": "ENST00000930052.1",
"protein_id": "ENSP00000600111.1",
"transcript_support_level": null,
"aa_start": 105,
"aa_end": null,
"aa_length": 244,
"cds_start": 314,
"cds_end": null,
"cds_length": 735,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000930052.1"
},
{
"aa_ref": "G",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"frameshift_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MDH2",
"gene_hgnc_id": 6971,
"hgvs_c": "c.275delG",
"hgvs_p": "p.Gly92fs",
"transcript": "NM_001282404.2",
"protein_id": "NP_001269333.1",
"transcript_support_level": null,
"aa_start": 92,
"aa_end": null,
"aa_length": 231,
"cds_start": 275,
"cds_end": null,
"cds_length": 696,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001282404.2"
},
{
"aa_ref": "G",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"frameshift_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MDH2",
"gene_hgnc_id": 6971,
"hgvs_c": "c.275delG",
"hgvs_p": "p.Gly92fs",
"transcript": "ENST00000443006.5",
"protein_id": "ENSP00000416929.1",
"transcript_support_level": 2,
"aa_start": 92,
"aa_end": null,
"aa_length": 231,
"cds_start": 275,
"cds_end": null,
"cds_length": 696,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000443006.5"
},
{
"aa_ref": "G",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"frameshift_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MDH2",
"gene_hgnc_id": 6971,
"hgvs_c": "c.272delG",
"hgvs_p": "p.Gly91fs",
"transcript": "ENST00000854578.1",
"protein_id": "ENSP00000524637.1",
"transcript_support_level": null,
"aa_start": 91,
"aa_end": null,
"aa_length": 230,
"cds_start": 272,
"cds_end": null,
"cds_length": 693,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000854578.1"
},
{
"aa_ref": "G",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"frameshift_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MDH2",
"gene_hgnc_id": 6971,
"hgvs_c": "c.233delG",
"hgvs_p": "p.Gly78fs",
"transcript": "ENST00000930053.1",
"protein_id": "ENSP00000600112.1",
"transcript_support_level": null,
"aa_start": 78,
"aa_end": null,
"aa_length": 217,
"cds_start": 233,
"cds_end": null,
"cds_length": 654,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000930053.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": 5,
"intron_rank_end": null,
"gene_symbol": "MDH2",
"gene_hgnc_id": 6971,
"hgvs_c": "c.556-784delG",
"hgvs_p": null,
"transcript": "ENST00000854581.1",
"protein_id": "ENSP00000524640.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 312,
"cds_start": null,
"cds_end": null,
"cds_length": 939,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000854581.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MDH2",
"gene_hgnc_id": 6971,
"hgvs_c": "n.172delG",
"hgvs_p": null,
"transcript": "ENST00000424167.2",
"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": "ENST00000424167.2"
}
],
"gene_symbol": "MDH2",
"gene_hgnc_id": 6971,
"dbsnp": "rs1057519567",
"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": null,
"computational_prediction_selected": null,
"computational_source_selected": null,
"splice_score_selected": 0.019999999552965164,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": null,
"bayesdelnoaf_prediction": null,
"phylop100way_score": 9.056,
"phylop100way_prediction": "Pathogenic",
"spliceai_max_score": 0.02,
"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": 12,
"acmg_classification": "Pathogenic",
"acmg_criteria": "PVS1,PM2,PP5_Moderate",
"acmg_by_gene": [
{
"score": 12,
"benign_score": 0,
"pathogenic_score": 12,
"criteria": [
"PVS1",
"PM2",
"PP5_Moderate"
],
"verdict": "Pathogenic",
"transcript": "NM_005918.4",
"gene_symbol": "MDH2",
"hgnc_id": 6971,
"effects": [
"frameshift_variant"
],
"inheritance_mode": "AR,AD",
"hgvs_c": "c.596delG",
"hgvs_p": "p.Gly199fs"
}
],
"clinvar_disease": " 51,Developmental and epileptic encephalopathy,Infantile encephalopathy",
"clinvar_classification": "Pathogenic",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "P:1",
"phenotype_combined": "Developmental and epileptic encephalopathy, 51|Infantile encephalopathy",
"pathogenicity_classification_combined": "Pathogenic",
"custom_annotations": null
}
],
"message": null
}