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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: 12-115991442-T-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=12&pos=115991442&ref=T&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "12",
"pos": 115991442,
"ref": "T",
"alt": "C",
"effect": "missense_variant",
"transcript": "ENST00000281928.9",
"consequences": [
{
"aa_ref": "K",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 17,
"exon_rank_end": null,
"exon_count": 31,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MED13L",
"gene_hgnc_id": 22962,
"hgvs_c": "c.3512A>G",
"hgvs_p": "p.Lys1171Arg",
"transcript": "NM_015335.5",
"protein_id": "NP_056150.1",
"transcript_support_level": null,
"aa_start": 1171,
"aa_end": null,
"aa_length": 2210,
"cds_start": 3512,
"cds_end": null,
"cds_length": 6633,
"cdna_start": 4074,
"cdna_end": null,
"cdna_length": 9885,
"mane_select": "ENST00000281928.9",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "K",
"aa_alt": "R",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 17,
"exon_rank_end": null,
"exon_count": 31,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MED13L",
"gene_hgnc_id": 22962,
"hgvs_c": "c.3512A>G",
"hgvs_p": "p.Lys1171Arg",
"transcript": "ENST00000281928.9",
"protein_id": "ENSP00000281928.3",
"transcript_support_level": 1,
"aa_start": 1171,
"aa_end": null,
"aa_length": 2210,
"cds_start": 3512,
"cds_end": null,
"cds_length": 6633,
"cdna_start": 4074,
"cdna_end": null,
"cdna_length": 9885,
"mane_select": "NM_015335.5",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "K",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 17,
"exon_rank_end": null,
"exon_count": 31,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MED13L",
"gene_hgnc_id": 22962,
"hgvs_c": "c.3512A>G",
"hgvs_p": "p.Lys1171Arg",
"transcript": "ENST00000650226.1",
"protein_id": "ENSP00000496981.1",
"transcript_support_level": null,
"aa_start": 1171,
"aa_end": null,
"aa_length": 2222,
"cds_start": 3512,
"cds_end": null,
"cds_length": 6669,
"cdna_start": 3555,
"cdna_end": null,
"cdna_length": 8717,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "K",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MED13L",
"gene_hgnc_id": 22962,
"hgvs_c": "c.1694A>G",
"hgvs_p": "p.Lys565Arg",
"transcript": "ENST00000649607.1",
"protein_id": "ENSP00000497064.1",
"transcript_support_level": null,
"aa_start": 565,
"aa_end": null,
"aa_length": 1604,
"cds_start": 1694,
"cds_end": null,
"cds_length": 4815,
"cdna_start": 1696,
"cdna_end": null,
"cdna_length": 6740,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "K",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MED13L",
"gene_hgnc_id": 22962,
"hgvs_c": "c.2939A>G",
"hgvs_p": "p.Lys980Arg",
"transcript": "ENST00000549786.2",
"protein_id": "ENSP00000446782.2",
"transcript_support_level": 2,
"aa_start": 980,
"aa_end": null,
"aa_length": 1544,
"cds_start": 2939,
"cds_end": null,
"cds_length": 4635,
"cdna_start": 2940,
"cdna_end": null,
"cdna_length": 5683,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "K",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 17,
"exon_rank_end": null,
"exon_count": 31,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MED13L",
"gene_hgnc_id": 22962,
"hgvs_c": "c.3509A>G",
"hgvs_p": "p.Lys1170Arg",
"transcript": "XM_017019090.2",
"protein_id": "XP_016874579.1",
"transcript_support_level": null,
"aa_start": 1170,
"aa_end": null,
"aa_length": 2209,
"cds_start": 3509,
"cds_end": null,
"cds_length": 6630,
"cdna_start": 4071,
"cdna_end": null,
"cdna_length": 9882,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "K",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 17,
"exon_rank_end": null,
"exon_count": 31,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MED13L",
"gene_hgnc_id": 22962,
"hgvs_c": "c.3482A>G",
"hgvs_p": "p.Lys1161Arg",
"transcript": "XM_047428605.1",
"protein_id": "XP_047284561.1",
"transcript_support_level": null,
"aa_start": 1161,
"aa_end": null,
"aa_length": 2200,
"cds_start": 3482,
"cds_end": null,
"cds_length": 6603,
"cdna_start": 3703,
"cdna_end": null,
"cdna_length": 9514,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "K",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 17,
"exon_rank_end": null,
"exon_count": 31,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MED13L",
"gene_hgnc_id": 22962,
"hgvs_c": "c.3479A>G",
"hgvs_p": "p.Lys1160Arg",
"transcript": "XM_047428607.1",
"protein_id": "XP_047284563.1",
"transcript_support_level": null,
"aa_start": 1160,
"aa_end": null,
"aa_length": 2199,
"cds_start": 3479,
"cds_end": null,
"cds_length": 6600,
"cdna_start": 3700,
"cdna_end": null,
"cdna_length": 9511,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "K",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 16,
"exon_rank_end": null,
"exon_count": 30,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MED13L",
"gene_hgnc_id": 22962,
"hgvs_c": "c.3110A>G",
"hgvs_p": "p.Lys1037Arg",
"transcript": "XM_047428608.1",
"protein_id": "XP_047284564.1",
"transcript_support_level": null,
"aa_start": 1037,
"aa_end": null,
"aa_length": 2076,
"cds_start": 3110,
"cds_end": null,
"cds_length": 6231,
"cdna_start": 3836,
"cdna_end": null,
"cdna_length": 9647,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "K",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 17,
"exon_rank_end": null,
"exon_count": 31,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MED13L",
"gene_hgnc_id": 22962,
"hgvs_c": "c.3110A>G",
"hgvs_p": "p.Lys1037Arg",
"transcript": "XM_047428609.1",
"protein_id": "XP_047284565.1",
"transcript_support_level": null,
"aa_start": 1037,
"aa_end": null,
"aa_length": 2076,
"cds_start": 3110,
"cds_end": null,
"cds_length": 6231,
"cdna_start": 7206,
"cdna_end": null,
"cdna_length": 13017,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "K",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 16,
"exon_rank_end": null,
"exon_count": 30,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MED13L",
"gene_hgnc_id": 22962,
"hgvs_c": "c.3110A>G",
"hgvs_p": "p.Lys1037Arg",
"transcript": "XM_047428610.1",
"protein_id": "XP_047284566.1",
"transcript_support_level": null,
"aa_start": 1037,
"aa_end": null,
"aa_length": 2076,
"cds_start": 3110,
"cds_end": null,
"cds_length": 6231,
"cdna_start": 5003,
"cdna_end": null,
"cdna_length": 10814,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "K",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 17,
"exon_rank_end": null,
"exon_count": 31,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MED13L",
"gene_hgnc_id": 22962,
"hgvs_c": "c.3110A>G",
"hgvs_p": "p.Lys1037Arg",
"transcript": "XM_047428611.1",
"protein_id": "XP_047284567.1",
"transcript_support_level": null,
"aa_start": 1037,
"aa_end": null,
"aa_length": 2076,
"cds_start": 3110,
"cds_end": null,
"cds_length": 6231,
"cdna_start": 5099,
"cdna_end": null,
"cdna_length": 10910,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MED13L",
"gene_hgnc_id": 22962,
"hgvs_c": "n.1880A>G",
"hgvs_p": null,
"transcript": "ENST00000648379.1",
"protein_id": null,
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 7496,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 14,
"exon_rank_end": null,
"exon_count": 28,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MED13L",
"gene_hgnc_id": 22962,
"hgvs_c": "n.3276A>G",
"hgvs_p": null,
"transcript": "ENST00000648737.1",
"protein_id": null,
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 8299,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MED13L",
"gene_hgnc_id": 22962,
"hgvs_c": "n.252A>G",
"hgvs_p": null,
"transcript": "ENST00000648825.1",
"protein_id": null,
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 6478,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MED13L",
"gene_hgnc_id": 22962,
"hgvs_c": "n.1523A>G",
"hgvs_p": null,
"transcript": "ENST00000648916.1",
"protein_id": null,
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 4720,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MED13L",
"gene_hgnc_id": 22962,
"hgvs_c": "n.8A>G",
"hgvs_p": null,
"transcript": "ENST00000649775.1",
"protein_id": "ENSP00000496984.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 4852,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"downstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MED13L",
"gene_hgnc_id": 22962,
"hgvs_c": "c.*238A>G",
"hgvs_p": null,
"transcript": "ENST00000548743.2",
"protein_id": "ENSP00000448553.2",
"transcript_support_level": 3,
"aa_start": null,
"aa_end": null,
"aa_length": 1080,
"cds_start": -4,
"cds_end": null,
"cds_length": 3244,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 3532,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "MED13L",
"gene_hgnc_id": 22962,
"dbsnp": "rs147863200",
"frequency_reference_population": 0.004303183,
"hom_count_reference_population": 23,
"allele_count_reference_population": 6946,
"gnomad_exomes_af": 0.00438206,
"gnomad_genomes_af": 0.00354601,
"gnomad_exomes_ac": 6406,
"gnomad_genomes_ac": 540,
"gnomad_exomes_homalt": 22,
"gnomad_genomes_homalt": 1,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.00980377197265625,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.1,
"revel_prediction": "Benign",
"alphamissense_score": 0.0732,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.54,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 2.519,
"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": -14,
"acmg_classification": "Benign",
"acmg_criteria": "PM1,BP4_Strong,BP6_Very_Strong,BS2",
"acmg_by_gene": [
{
"score": -14,
"benign_score": 16,
"pathogenic_score": 2,
"criteria": [
"PM1",
"BP4_Strong",
"BP6_Very_Strong",
"BS2"
],
"verdict": "Benign",
"transcript": "ENST00000281928.9",
"gene_symbol": "MED13L",
"hgnc_id": 22962,
"effects": [
"missense_variant"
],
"inheritance_mode": "AD",
"hgvs_c": "c.3512A>G",
"hgvs_p": "p.Lys1171Arg"
}
],
"clinvar_disease": " dextro-looped,Cardiac anomalies - developmental delay - facial dysmorphism syndrome,MED13L-related disorder,Transposition of the great arteries,not provided,not specified",
"clinvar_classification": "Benign/Likely benign",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "LB:4 B:3",
"phenotype_combined": "not specified|not provided|Transposition of the great arteries, dextro-looped|Cardiac anomalies - developmental delay - facial dysmorphism syndrome|MED13L-related disorder",
"pathogenicity_classification_combined": "Benign/Likely benign",
"custom_annotations": null
}
],
"message": null
}