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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: 12-115982613-G-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=12&pos=115982613&ref=G&alt=C&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 6,
"criteria": [
"PM2",
"BP4_Strong",
"BP6_Moderate"
],
"effects": [
"intron_variant"
],
"gene_symbol": "MED13L",
"hgnc_id": 22962,
"hgvs_c": "c.4956-10C>G",
"hgvs_p": null,
"inheritance_mode": "AD",
"pathogenic_score": 2,
"score": -4,
"transcript": "NM_015335.5",
"verdict": "Likely_benign"
}
],
"acmg_classification": "Likely_benign",
"acmg_criteria": "PM2,BP4_Strong,BP6_Moderate",
"acmg_score": -4,
"allele_count_reference_population": 1,
"alphamissense_prediction": null,
"alphamissense_score": null,
"alt": "C",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Benign",
"bayesdelnoaf_score": -0.82,
"chr": "12",
"clinvar_classification": "Likely benign",
"clinvar_disease": " dextro-looped,Transposition of the great arteries",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "LB:1",
"computational_prediction_selected": "Benign",
"computational_score_selected": -0.8199999928474426,
"computational_source_selected": "BayesDel_noAF",
"consequences": [
{
"aa_alt": null,
"aa_end": null,
"aa_length": 2210,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 9885,
"cdna_start": null,
"cds_end": null,
"cds_length": 6633,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 31,
"exon_rank": null,
"exon_rank_end": null,
"feature": "NM_015335.5",
"gene_hgnc_id": 22962,
"gene_symbol": "MED13L",
"hgvs_c": "c.4956-10C>G",
"hgvs_p": null,
"intron_rank": 21,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000281928.9",
"protein_coding": true,
"protein_id": "NP_056150.1",
"strand": false,
"transcript": "NM_015335.5",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 2210,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 9885,
"cdna_start": null,
"cds_end": null,
"cds_length": 6633,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 31,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000281928.9",
"gene_hgnc_id": 22962,
"gene_symbol": "MED13L",
"hgvs_c": "c.4956-10C>G",
"hgvs_p": null,
"intron_rank": 21,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_015335.5",
"protein_coding": true,
"protein_id": "ENSP00000281928.3",
"strand": false,
"transcript": "ENST00000281928.9",
"transcript_support_level": 1
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 2222,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 8717,
"cdna_start": null,
"cds_end": null,
"cds_length": 6669,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 31,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000650226.1",
"gene_hgnc_id": 22962,
"gene_symbol": "MED13L",
"hgvs_c": "c.4956-10C>G",
"hgvs_p": null,
"intron_rank": 21,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000496981.1",
"strand": false,
"transcript": "ENST00000650226.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 1604,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 6740,
"cdna_start": null,
"cds_end": null,
"cds_length": 4815,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 22,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000649607.1",
"gene_hgnc_id": 22962,
"gene_symbol": "MED13L",
"hgvs_c": "c.3138-10C>G",
"hgvs_p": null,
"intron_rank": 12,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000497064.1",
"strand": false,
"transcript": "ENST00000649607.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 1544,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5683,
"cdna_start": null,
"cds_end": null,
"cds_length": 4635,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 18,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000549786.2",
"gene_hgnc_id": 22962,
"gene_symbol": "MED13L",
"hgvs_c": "c.4383-10C>G",
"hgvs_p": null,
"intron_rank": 17,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000446782.2",
"strand": false,
"transcript": "ENST00000549786.2",
"transcript_support_level": 2
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 2209,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 9882,
"cdna_start": null,
"cds_end": null,
"cds_length": 6630,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 31,
"exon_rank": null,
"exon_rank_end": null,
"feature": "XM_017019090.2",
"gene_hgnc_id": 22962,
"gene_symbol": "MED13L",
"hgvs_c": "c.4953-10C>G",
"hgvs_p": null,
"intron_rank": 21,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_016874579.1",
"strand": false,
"transcript": "XM_017019090.2",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 2200,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 9514,
"cdna_start": null,
"cds_end": null,
"cds_length": 6603,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 31,
"exon_rank": null,
"exon_rank_end": null,
"feature": "XM_047428605.1",
"gene_hgnc_id": 22962,
"gene_symbol": "MED13L",
"hgvs_c": "c.4926-10C>G",
"hgvs_p": null,
"intron_rank": 21,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_047284561.1",
"strand": false,
"transcript": "XM_047428605.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 2199,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 9511,
"cdna_start": null,
"cds_end": null,
"cds_length": 6600,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 31,
"exon_rank": null,
"exon_rank_end": null,
"feature": "XM_047428607.1",
"gene_hgnc_id": 22962,
"gene_symbol": "MED13L",
"hgvs_c": "c.4923-10C>G",
"hgvs_p": null,
"intron_rank": 21,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_047284563.1",
"strand": false,
"transcript": "XM_047428607.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 2076,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 9647,
"cdna_start": null,
"cds_end": null,
"cds_length": 6231,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 30,
"exon_rank": null,
"exon_rank_end": null,
"feature": "XM_047428608.1",
"gene_hgnc_id": 22962,
"gene_symbol": "MED13L",
"hgvs_c": "c.4554-10C>G",
"hgvs_p": null,
"intron_rank": 20,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_047284564.1",
"strand": false,
"transcript": "XM_047428608.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 2076,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 13017,
"cdna_start": null,
"cds_end": null,
"cds_length": 6231,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 31,
"exon_rank": null,
"exon_rank_end": null,
"feature": "XM_047428609.1",
"gene_hgnc_id": 22962,
"gene_symbol": "MED13L",
"hgvs_c": "c.4554-10C>G",
"hgvs_p": null,
"intron_rank": 21,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_047284565.1",
"strand": false,
"transcript": "XM_047428609.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 2076,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 10814,
"cdna_start": null,
"cds_end": null,
"cds_length": 6231,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 30,
"exon_rank": null,
"exon_rank_end": null,
"feature": "XM_047428610.1",
"gene_hgnc_id": 22962,
"gene_symbol": "MED13L",
"hgvs_c": "c.4554-10C>G",
"hgvs_p": null,
"intron_rank": 20,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_047284566.1",
"strand": false,
"transcript": "XM_047428610.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 2076,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 10910,
"cdna_start": null,
"cds_end": null,
"cds_length": 6231,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 31,
"exon_rank": null,
"exon_rank_end": null,
"feature": "XM_047428611.1",
"gene_hgnc_id": 22962,
"gene_symbol": "MED13L",
"hgvs_c": "c.4554-10C>G",
"hgvs_p": null,
"intron_rank": 21,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_047284567.1",
"strand": false,
"transcript": "XM_047428611.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "retained_intron",
"canonical": false,
"cdna_end": null,
"cdna_length": 3237,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 2,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000649146.1",
"gene_hgnc_id": 22962,
"gene_symbol": "MED13L",
"hgvs_c": "n.2189C>G",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": false,
"transcript": "ENST00000649146.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "retained_intron",
"canonical": false,
"cdna_end": null,
"cdna_length": 7496,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 18,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000648379.1",
"gene_hgnc_id": 22962,
"gene_symbol": "MED13L",
"hgvs_c": "n.3324-10C>G",
"hgvs_p": null,
"intron_rank": 8,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": false,
"transcript": "ENST00000648379.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "retained_intron",
"canonical": false,
"cdna_end": null,
"cdna_length": 8299,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 28,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000648737.1",
"gene_hgnc_id": 22962,
"gene_symbol": "MED13L",
"hgvs_c": "n.4720-10C>G",
"hgvs_p": null,
"intron_rank": 18,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": false,
"transcript": "ENST00000648737.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "retained_intron",
"canonical": false,
"cdna_end": null,
"cdna_length": 6478,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 14,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000648825.1",
"gene_hgnc_id": 22962,
"gene_symbol": "MED13L",
"hgvs_c": "n.1696-10C>G",
"hgvs_p": null,
"intron_rank": 5,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": false,
"transcript": "ENST00000648825.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "retained_intron",
"canonical": false,
"cdna_end": null,
"cdna_length": 4720,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 19,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000648916.1",
"gene_hgnc_id": 22962,
"gene_symbol": "MED13L",
"hgvs_c": "n.2967-10C>G",
"hgvs_p": null,
"intron_rank": 9,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": false,
"transcript": "ENST00000648916.1",
"transcript_support_level": null
},
{
"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": 4852,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 14,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000649775.1",
"gene_hgnc_id": 22962,
"gene_symbol": "MED13L",
"hgvs_c": "n.1452-18C>G",
"hgvs_p": null,
"intron_rank": 5,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000496984.1",
"strand": false,
"transcript": "ENST00000649775.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "retained_intron",
"canonical": false,
"cdna_end": null,
"cdna_length": 665,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"upstream_gene_variant"
],
"exon_count": 2,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000552340.1",
"gene_hgnc_id": 22962,
"gene_symbol": "MED13L",
"hgvs_c": "n.-23C>G",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": true,
"transcript": "ENST00000552340.1",
"transcript_support_level": 3
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": "Benign",
"dbscsnv_ada_score": 0.0013139045136659,
"dbsnp": "rs1060504701",
"effect": "intron_variant",
"frequency_reference_population": 0.0000065713384,
"gene_hgnc_id": 22962,
"gene_symbol": "MED13L",
"gnomad_exomes_ac": null,
"gnomad_exomes_af": null,
"gnomad_exomes_homalt": null,
"gnomad_genomes_ac": 1,
"gnomad_genomes_af": 0.00000657134,
"gnomad_genomes_homalt": 0,
"gnomad_mito_heteroplasmic": null,
"gnomad_mito_homoplasmic": null,
"hom_count_reference_population": 0,
"mitotip_prediction": null,
"mitotip_score": null,
"pathogenicity_classification_combined": "Likely benign",
"phenotype_combined": "Transposition of the great arteries, dextro-looped",
"phylop100way_prediction": "Benign",
"phylop100way_score": -0.298,
"pos": 115982613,
"ref": "G",
"revel_prediction": null,
"revel_score": null,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0.07000000029802322,
"splice_source_selected": "dbscSNV1_RF",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0.14,
"transcript": "NM_015335.5"
}
]
}