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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: 3-12572230-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=3&pos=12572230&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "3",
"pos": 12572230,
"ref": "G",
"alt": "A",
"effect": "missense_variant",
"transcript": "NM_014160.5",
"consequences": [
{
"aa_ref": "E",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MKRN2",
"gene_hgnc_id": 7113,
"hgvs_c": "c.499G>A",
"hgvs_p": "p.Glu167Lys",
"transcript": "NM_014160.5",
"protein_id": "NP_054879.3",
"transcript_support_level": null,
"aa_start": 167,
"aa_end": null,
"aa_length": 416,
"cds_start": 499,
"cds_end": null,
"cds_length": 1251,
"cdna_start": 563,
"cdna_end": null,
"cdna_length": 2775,
"mane_select": "ENST00000170447.12",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "K",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MKRN2",
"gene_hgnc_id": 7113,
"hgvs_c": "c.499G>A",
"hgvs_p": "p.Glu167Lys",
"transcript": "ENST00000170447.12",
"protein_id": "ENSP00000170447.7",
"transcript_support_level": 1,
"aa_start": 167,
"aa_end": null,
"aa_length": 416,
"cds_start": 499,
"cds_end": null,
"cds_length": 1251,
"cdna_start": 563,
"cdna_end": null,
"cdna_length": 2775,
"mane_select": "NM_014160.5",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MKRN2",
"gene_hgnc_id": 7113,
"hgvs_c": "c.532G>A",
"hgvs_p": "p.Glu178Lys",
"transcript": "ENST00000677142.1",
"protein_id": "ENSP00000504455.1",
"transcript_support_level": null,
"aa_start": 178,
"aa_end": null,
"aa_length": 427,
"cds_start": 532,
"cds_end": null,
"cds_length": 1284,
"cdna_start": 730,
"cdna_end": null,
"cdna_length": 5021,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MKRN2",
"gene_hgnc_id": 7113,
"hgvs_c": "c.493G>A",
"hgvs_p": "p.Glu165Lys",
"transcript": "ENST00000448482.1",
"protein_id": "ENSP00000397983.1",
"transcript_support_level": 5,
"aa_start": 165,
"aa_end": null,
"aa_length": 414,
"cds_start": 493,
"cds_end": null,
"cds_length": 1245,
"cdna_start": 554,
"cdna_end": null,
"cdna_length": 1679,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MKRN2",
"gene_hgnc_id": 7113,
"hgvs_c": "c.481G>A",
"hgvs_p": "p.Glu161Lys",
"transcript": "ENST00000676541.1",
"protein_id": "ENSP00000503730.1",
"transcript_support_level": null,
"aa_start": 161,
"aa_end": null,
"aa_length": 410,
"cds_start": 481,
"cds_end": null,
"cds_length": 1233,
"cdna_start": 900,
"cdna_end": null,
"cdna_length": 5191,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MKRN2",
"gene_hgnc_id": 7113,
"hgvs_c": "c.370G>A",
"hgvs_p": "p.Glu124Lys",
"transcript": "NM_001271707.2",
"protein_id": "NP_001258636.1",
"transcript_support_level": null,
"aa_start": 124,
"aa_end": null,
"aa_length": 373,
"cds_start": 370,
"cds_end": null,
"cds_length": 1122,
"cdna_start": 434,
"cdna_end": null,
"cdna_length": 2646,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MKRN2",
"gene_hgnc_id": 7113,
"hgvs_c": "c.370G>A",
"hgvs_p": "p.Glu124Lys",
"transcript": "ENST00000411987.5",
"protein_id": "ENSP00000396340.1",
"transcript_support_level": 2,
"aa_start": 124,
"aa_end": null,
"aa_length": 373,
"cds_start": 370,
"cds_end": null,
"cds_length": 1122,
"cdna_start": 434,
"cdna_end": null,
"cdna_length": 1436,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MKRN2",
"gene_hgnc_id": 7113,
"hgvs_c": "n.593G>A",
"hgvs_p": null,
"transcript": "ENST00000676544.1",
"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": 4412,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MKRN2",
"gene_hgnc_id": 7113,
"hgvs_c": "n.*395G>A",
"hgvs_p": null,
"transcript": "ENST00000676701.1",
"protein_id": "ENSP00000503305.1",
"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": 3021,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MKRN2",
"gene_hgnc_id": 7113,
"hgvs_c": "n.593G>A",
"hgvs_p": null,
"transcript": "ENST00000677237.1",
"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": 2510,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MKRN2",
"gene_hgnc_id": 7113,
"hgvs_c": "n.499G>A",
"hgvs_p": null,
"transcript": "ENST00000677816.1",
"protein_id": "ENSP00000502893.1",
"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": 3855,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MKRN2",
"gene_hgnc_id": 7113,
"hgvs_c": "n.593G>A",
"hgvs_p": null,
"transcript": "ENST00000677941.1",
"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": 3610,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MKRN2",
"gene_hgnc_id": 7113,
"hgvs_c": "n.*395G>A",
"hgvs_p": null,
"transcript": "ENST00000676701.1",
"protein_id": "ENSP00000503305.1",
"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": 3021,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": 4,
"intron_rank_end": null,
"gene_symbol": "MKRN2",
"gene_hgnc_id": 7113,
"hgvs_c": "n.*265+121G>A",
"hgvs_p": null,
"transcript": "ENST00000679143.1",
"protein_id": "ENSP00000504009.1",
"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": 2745,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"upstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MKRN2",
"gene_hgnc_id": 7113,
"hgvs_c": "n.-45G>A",
"hgvs_p": null,
"transcript": "ENST00000677798.1",
"protein_id": "ENSP00000503754.1",
"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": 941,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "MKRN2",
"gene_hgnc_id": 7113,
"dbsnp": "rs373294185",
"frequency_reference_population": 0.000005472413,
"hom_count_reference_population": 0,
"allele_count_reference_population": 8,
"gnomad_exomes_af": 0.00000547241,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": 8,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.08329308032989502,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.133,
"revel_prediction": "Benign",
"alphamissense_score": 0.0811,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.59,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 4.07,
"phylop100way_prediction": "Uncertain_significance",
"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": 0,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2,BP4_Moderate",
"acmg_by_gene": [
{
"score": 0,
"benign_score": 2,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4_Moderate"
],
"verdict": "Uncertain_significance",
"transcript": "NM_014160.5",
"gene_symbol": "MKRN2",
"hgnc_id": 7113,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.499G>A",
"hgvs_p": "p.Glu167Lys"
}
],
"clinvar_disease": "not specified",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"phenotype_combined": "not specified",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}