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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: 10-80289576-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=10&pos=80289576&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 20,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong",
"BS1",
"BS2"
],
"effects": [
"5_prime_UTR_variant"
],
"gene_symbol": "MAT1A",
"hgnc_id": 6903,
"hgvs_c": "c.-153C>T",
"hgvs_p": null,
"inheritance_mode": "AR,AD",
"pathogenic_score": 0,
"score": -20,
"transcript": "NM_000429.3",
"verdict": "Benign"
}
],
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6_Very_Strong,BS1,BS2",
"acmg_score": -20,
"allele_count_reference_population": 18832,
"alphamissense_prediction": null,
"alphamissense_score": null,
"alt": "A",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Benign",
"bayesdelnoaf_score": -0.7,
"chr": "10",
"clinvar_classification": "Benign",
"clinvar_disease": "Hepatic methionine adenosyltransferase deficiency,not provided",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "B:2",
"computational_prediction_selected": "Benign",
"computational_score_selected": -0.699999988079071,
"computational_source_selected": "BayesDel_noAF",
"consequences": [
{
"aa_alt": null,
"aa_end": null,
"aa_length": 395,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3384,
"cdna_start": null,
"cds_end": null,
"cds_length": 1188,
"cds_start": null,
"consequences": [
"5_prime_UTR_variant"
],
"exon_count": 9,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "NM_000429.3",
"gene_hgnc_id": 6903,
"gene_symbol": "MAT1A",
"hgvs_c": "c.-153C>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000372213.8",
"protein_coding": true,
"protein_id": "NP_000420.1",
"strand": false,
"transcript": "NM_000429.3",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 395,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 3384,
"cdna_start": null,
"cds_end": null,
"cds_length": 1188,
"cds_start": null,
"consequences": [
"5_prime_UTR_variant"
],
"exon_count": 9,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "ENST00000372213.8",
"gene_hgnc_id": 6903,
"gene_symbol": "MAT1A",
"hgvs_c": "c.-153C>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_000429.3",
"protein_coding": true,
"protein_id": "ENSP00000361287.3",
"strand": false,
"transcript": "ENST00000372213.8",
"transcript_support_level": 1
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 467,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3596,
"cdna_start": null,
"cds_end": null,
"cds_length": 1404,
"cds_start": null,
"consequences": [
"5_prime_UTR_variant"
],
"exon_count": 9,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "ENST00000871627.1",
"gene_hgnc_id": 6903,
"gene_symbol": "MAT1A",
"hgvs_c": "c.-153C>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000541686.1",
"strand": false,
"transcript": "ENST00000871627.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 450,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3548,
"cdna_start": null,
"cds_end": null,
"cds_length": 1353,
"cds_start": null,
"consequences": [
"5_prime_UTR_variant"
],
"exon_count": 9,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "ENST00000871624.1",
"gene_hgnc_id": 6903,
"gene_symbol": "MAT1A",
"hgvs_c": "c.-153C>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000541683.1",
"strand": false,
"transcript": "ENST00000871624.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 436,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3504,
"cdna_start": null,
"cds_end": null,
"cds_length": 1311,
"cds_start": null,
"consequences": [
"5_prime_UTR_variant"
],
"exon_count": 9,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "ENST00000871626.1",
"gene_hgnc_id": 6903,
"gene_symbol": "MAT1A",
"hgvs_c": "c.-153C>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000541685.1",
"strand": false,
"transcript": "ENST00000871626.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 402,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3404,
"cdna_start": null,
"cds_end": null,
"cds_length": 1209,
"cds_start": null,
"consequences": [
"5_prime_UTR_variant"
],
"exon_count": 9,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "ENST00000871625.1",
"gene_hgnc_id": 6903,
"gene_symbol": "MAT1A",
"hgvs_c": "c.-153C>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000541684.1",
"strand": false,
"transcript": "ENST00000871625.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 393,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3382,
"cdna_start": null,
"cds_end": null,
"cds_length": 1182,
"cds_start": null,
"consequences": [
"5_prime_UTR_variant"
],
"exon_count": 9,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "ENST00000871620.1",
"gene_hgnc_id": 6903,
"gene_symbol": "MAT1A",
"hgvs_c": "c.-153C>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000541679.1",
"strand": false,
"transcript": "ENST00000871620.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 373,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3319,
"cdna_start": null,
"cds_end": null,
"cds_length": 1122,
"cds_start": null,
"consequences": [
"5_prime_UTR_variant"
],
"exon_count": 9,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "ENST00000871621.1",
"gene_hgnc_id": 6903,
"gene_symbol": "MAT1A",
"hgvs_c": "c.-153C>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000541680.1",
"strand": false,
"transcript": "ENST00000871621.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 370,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5389,
"cdna_start": null,
"cds_end": null,
"cds_length": 1113,
"cds_start": null,
"consequences": [
"5_prime_UTR_variant"
],
"exon_count": 10,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000871619.1",
"gene_hgnc_id": 6903,
"gene_symbol": "MAT1A",
"hgvs_c": "c.-153C>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000541678.1",
"strand": false,
"transcript": "ENST00000871619.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 334,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3200,
"cdna_start": null,
"cds_end": null,
"cds_length": 1005,
"cds_start": null,
"consequences": [
"5_prime_UTR_variant"
],
"exon_count": 8,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "ENST00000871623.1",
"gene_hgnc_id": 6903,
"gene_symbol": "MAT1A",
"hgvs_c": "c.-153C>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000541682.1",
"strand": false,
"transcript": "ENST00000871623.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 329,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3187,
"cdna_start": null,
"cds_end": null,
"cds_length": 990,
"cds_start": null,
"consequences": [
"5_prime_UTR_variant"
],
"exon_count": 8,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "ENST00000871622.1",
"gene_hgnc_id": 6903,
"gene_symbol": "MAT1A",
"hgvs_c": "c.-153C>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000541681.1",
"strand": false,
"transcript": "ENST00000871622.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 420,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3334,
"cdna_start": null,
"cds_end": null,
"cds_length": 1263,
"cds_start": null,
"consequences": [
"upstream_gene_variant"
],
"exon_count": 9,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000871628.1",
"gene_hgnc_id": 6903,
"gene_symbol": "MAT1A",
"hgvs_c": "c.-153C>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000541687.1",
"strand": true,
"transcript": "ENST00000871628.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 144,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 435,
"cdna_start": null,
"cds_end": null,
"cds_length": 435,
"cds_start": null,
"consequences": [
"upstream_gene_variant"
],
"exon_count": 5,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000455001.1",
"gene_hgnc_id": 6903,
"gene_symbol": "MAT1A",
"hgvs_c": "c.-219C>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000414961.1",
"strand": true,
"transcript": "ENST00000455001.1",
"transcript_support_level": 5
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs11595587",
"effect": "5_prime_UTR_variant",
"frequency_reference_population": 0.027097339,
"gene_hgnc_id": 6903,
"gene_symbol": "MAT1A",
"gnomad_exomes_ac": 15075,
"gnomad_exomes_af": 0.0277698,
"gnomad_exomes_homalt": 263,
"gnomad_genomes_ac": 3757,
"gnomad_genomes_af": 0.0246976,
"gnomad_genomes_homalt": 77,
"gnomad_mito_heteroplasmic": null,
"gnomad_mito_homoplasmic": null,
"hom_count_reference_population": 340,
"mitotip_prediction": null,
"mitotip_score": null,
"pathogenicity_classification_combined": "Benign",
"phenotype_combined": "Hepatic methionine adenosyltransferase deficiency|not provided",
"phylop100way_prediction": "Benign",
"phylop100way_score": -0.127,
"pos": 80289576,
"ref": "G",
"revel_prediction": null,
"revel_score": null,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0,
"transcript": "NM_000429.3"
}
]
}