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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: 10-80280296-A-G (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=10&pos=80280296&ref=A&alt=G&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "10",
"pos": 80280296,
"ref": "A",
"alt": "G",
"effect": "synonymous_variant",
"transcript": "NM_000429.3",
"consequences": [
{
"aa_ref": "A",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MAT1A",
"gene_hgnc_id": 6903,
"hgvs_c": "c.426T>C",
"hgvs_p": "p.Ala142Ala",
"transcript": "NM_000429.3",
"protein_id": "NP_000420.1",
"transcript_support_level": null,
"aa_start": 142,
"aa_end": null,
"aa_length": 395,
"cds_start": 426,
"cds_end": null,
"cds_length": 1188,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000372213.8",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_000429.3"
},
{
"aa_ref": "A",
"aa_alt": "A",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MAT1A",
"gene_hgnc_id": 6903,
"hgvs_c": "c.426T>C",
"hgvs_p": "p.Ala142Ala",
"transcript": "ENST00000372213.8",
"protein_id": "ENSP00000361287.3",
"transcript_support_level": 1,
"aa_start": 142,
"aa_end": null,
"aa_length": 395,
"cds_start": 426,
"cds_end": null,
"cds_length": 1188,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_000429.3",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000372213.8"
},
{
"aa_ref": "A",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MAT1A",
"gene_hgnc_id": 6903,
"hgvs_c": "c.426T>C",
"hgvs_p": "p.Ala142Ala",
"transcript": "ENST00000871627.1",
"protein_id": "ENSP00000541686.1",
"transcript_support_level": null,
"aa_start": 142,
"aa_end": null,
"aa_length": 467,
"cds_start": 426,
"cds_end": null,
"cds_length": 1404,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000871627.1"
},
{
"aa_ref": "A",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MAT1A",
"gene_hgnc_id": 6903,
"hgvs_c": "c.591T>C",
"hgvs_p": "p.Ala197Ala",
"transcript": "ENST00000871624.1",
"protein_id": "ENSP00000541683.1",
"transcript_support_level": null,
"aa_start": 197,
"aa_end": null,
"aa_length": 450,
"cds_start": 591,
"cds_end": null,
"cds_length": 1353,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000871624.1"
},
{
"aa_ref": "A",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MAT1A",
"gene_hgnc_id": 6903,
"hgvs_c": "c.549T>C",
"hgvs_p": "p.Ala183Ala",
"transcript": "ENST00000871626.1",
"protein_id": "ENSP00000541685.1",
"transcript_support_level": null,
"aa_start": 183,
"aa_end": null,
"aa_length": 436,
"cds_start": 549,
"cds_end": null,
"cds_length": 1311,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000871626.1"
},
{
"aa_ref": "A",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MAT1A",
"gene_hgnc_id": 6903,
"hgvs_c": "c.426T>C",
"hgvs_p": "p.Ala142Ala",
"transcript": "ENST00000871628.1",
"protein_id": "ENSP00000541687.1",
"transcript_support_level": null,
"aa_start": 142,
"aa_end": null,
"aa_length": 420,
"cds_start": 426,
"cds_end": null,
"cds_length": 1263,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000871628.1"
},
{
"aa_ref": "A",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MAT1A",
"gene_hgnc_id": 6903,
"hgvs_c": "c.447T>C",
"hgvs_p": "p.Ala149Ala",
"transcript": "ENST00000871625.1",
"protein_id": "ENSP00000541684.1",
"transcript_support_level": null,
"aa_start": 149,
"aa_end": null,
"aa_length": 402,
"cds_start": 447,
"cds_end": null,
"cds_length": 1209,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000871625.1"
},
{
"aa_ref": "A",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MAT1A",
"gene_hgnc_id": 6903,
"hgvs_c": "c.420T>C",
"hgvs_p": "p.Ala140Ala",
"transcript": "ENST00000871620.1",
"protein_id": "ENSP00000541679.1",
"transcript_support_level": null,
"aa_start": 140,
"aa_end": null,
"aa_length": 393,
"cds_start": 420,
"cds_end": null,
"cds_length": 1182,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000871620.1"
},
{
"aa_ref": "A",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MAT1A",
"gene_hgnc_id": 6903,
"hgvs_c": "c.426T>C",
"hgvs_p": "p.Ala142Ala",
"transcript": "ENST00000871621.1",
"protein_id": "ENSP00000541680.1",
"transcript_support_level": null,
"aa_start": 142,
"aa_end": null,
"aa_length": 373,
"cds_start": 426,
"cds_end": null,
"cds_length": 1122,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000871621.1"
},
{
"aa_ref": "A",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MAT1A",
"gene_hgnc_id": 6903,
"hgvs_c": "c.426T>C",
"hgvs_p": "p.Ala142Ala",
"transcript": "ENST00000871619.1",
"protein_id": "ENSP00000541678.1",
"transcript_support_level": null,
"aa_start": 142,
"aa_end": null,
"aa_length": 370,
"cds_start": 426,
"cds_end": null,
"cds_length": 1113,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000871619.1"
},
{
"aa_ref": "A",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MAT1A",
"gene_hgnc_id": 6903,
"hgvs_c": "c.426T>C",
"hgvs_p": "p.Ala142Ala",
"transcript": "ENST00000871623.1",
"protein_id": "ENSP00000541682.1",
"transcript_support_level": null,
"aa_start": 142,
"aa_end": null,
"aa_length": 334,
"cds_start": 426,
"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": "ENST00000871623.1"
},
{
"aa_ref": "A",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MAT1A",
"gene_hgnc_id": 6903,
"hgvs_c": "c.303T>C",
"hgvs_p": "p.Ala101Ala",
"transcript": "ENST00000871622.1",
"protein_id": "ENSP00000541681.1",
"transcript_support_level": null,
"aa_start": 101,
"aa_end": null,
"aa_length": 329,
"cds_start": 303,
"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": "ENST00000871622.1"
},
{
"aa_ref": "A",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MAT1A",
"gene_hgnc_id": 6903,
"hgvs_c": "c.237T>C",
"hgvs_p": "p.Ala79Ala",
"transcript": "ENST00000455001.1",
"protein_id": "ENSP00000414961.1",
"transcript_support_level": 5,
"aa_start": 79,
"aa_end": null,
"aa_length": 144,
"cds_start": 237,
"cds_end": null,
"cds_length": 435,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000455001.1"
}
],
"gene_symbol": "MAT1A",
"gene_hgnc_id": 6903,
"dbsnp": "rs1143694",
"frequency_reference_population": 0.70642513,
"hom_count_reference_population": 409105,
"allele_count_reference_population": 1139937,
"gnomad_exomes_af": 0.699761,
"gnomad_genomes_af": 0.770558,
"gnomad_exomes_ac": 1022897,
"gnomad_genomes_ac": 117040,
"gnomad_exomes_homalt": 362787,
"gnomad_genomes_homalt": 46318,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": -0.5799999833106995,
"computational_prediction_selected": "Benign",
"computational_source_selected": "BayesDel_noAF",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.58,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 0.585,
"phylop100way_prediction": "Benign",
"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": -21,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6_Very_Strong,BP7,BA1",
"acmg_by_gene": [
{
"score": -21,
"benign_score": 21,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong",
"BP7",
"BA1"
],
"verdict": "Benign",
"transcript": "NM_000429.3",
"gene_symbol": "MAT1A",
"hgnc_id": 6903,
"effects": [
"synonymous_variant"
],
"inheritance_mode": "AR,AD",
"hgvs_c": "c.426T>C",
"hgvs_p": "p.Ala142Ala"
}
],
"clinvar_disease": "Hepatic methionine adenosyltransferase deficiency,not provided,not specified",
"clinvar_classification": "Benign",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "B:5",
"phenotype_combined": "not specified|Hepatic methionine adenosyltransferase deficiency|not provided",
"pathogenicity_classification_combined": "Benign",
"custom_annotations": null
}
],
"message": null
}