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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: 12-123256877-T-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=12&pos=123256877&ref=T&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "12",
"pos": 123256877,
"ref": "T",
"alt": "C",
"effect": "missense_variant",
"transcript": "ENST00000253233.6",
"consequences": [
{
"aa_ref": "V",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MTRFR",
"gene_hgnc_id": 26784,
"hgvs_c": "c.347T>C",
"hgvs_p": "p.Val116Ala",
"transcript": "NM_152269.5",
"protein_id": "NP_689482.1",
"transcript_support_level": null,
"aa_start": 116,
"aa_end": null,
"aa_length": 166,
"cds_start": 347,
"cds_end": null,
"cds_length": 501,
"cdna_start": 471,
"cdna_end": null,
"cdna_length": 1554,
"mane_select": "ENST00000253233.6",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "A",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MTRFR",
"gene_hgnc_id": 26784,
"hgvs_c": "c.347T>C",
"hgvs_p": "p.Val116Ala",
"transcript": "ENST00000253233.6",
"protein_id": "ENSP00000253233.1",
"transcript_support_level": 1,
"aa_start": 116,
"aa_end": null,
"aa_length": 166,
"cds_start": 347,
"cds_end": null,
"cds_length": 501,
"cdna_start": 471,
"cdna_end": null,
"cdna_length": 1554,
"mane_select": "NM_152269.5",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MTRFR",
"gene_hgnc_id": 26784,
"hgvs_c": "c.347T>C",
"hgvs_p": "p.Val116Ala",
"transcript": "NM_001143905.2",
"protein_id": "NP_001137377.1",
"transcript_support_level": null,
"aa_start": 116,
"aa_end": null,
"aa_length": 166,
"cds_start": 347,
"cds_end": null,
"cds_length": 501,
"cdna_start": 526,
"cdna_end": null,
"cdna_length": 1608,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MTRFR",
"gene_hgnc_id": 26784,
"hgvs_c": "c.347T>C",
"hgvs_p": "p.Val116Ala",
"transcript": "NM_001194995.1",
"protein_id": "NP_001181924.1",
"transcript_support_level": null,
"aa_start": 116,
"aa_end": null,
"aa_length": 166,
"cds_start": 347,
"cds_end": null,
"cds_length": 501,
"cdna_start": 819,
"cdna_end": null,
"cdna_length": 1901,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MTRFR",
"gene_hgnc_id": 26784,
"hgvs_c": "c.347T>C",
"hgvs_p": "p.Val116Ala",
"transcript": "ENST00000366329.7",
"protein_id": "ENSP00000390647.1",
"transcript_support_level": 2,
"aa_start": 116,
"aa_end": null,
"aa_length": 166,
"cds_start": 347,
"cds_end": null,
"cds_length": 501,
"cdna_start": 854,
"cdna_end": null,
"cdna_length": 2056,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MTRFR",
"gene_hgnc_id": 26784,
"hgvs_c": "c.347T>C",
"hgvs_p": "p.Val116Ala",
"transcript": "ENST00000429587.2",
"protein_id": "ENSP00000391513.2",
"transcript_support_level": 2,
"aa_start": 116,
"aa_end": null,
"aa_length": 166,
"cds_start": 347,
"cds_end": null,
"cds_length": 501,
"cdna_start": 632,
"cdna_end": null,
"cdna_length": 1326,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MTRFR",
"gene_hgnc_id": 26784,
"hgvs_c": "c.347T>C",
"hgvs_p": "p.Val116Ala",
"transcript": "ENST00000536130.2",
"protein_id": "ENSP00000443072.2",
"transcript_support_level": 3,
"aa_start": 116,
"aa_end": null,
"aa_length": 166,
"cds_start": 347,
"cds_end": null,
"cds_length": 501,
"cdna_start": 630,
"cdna_end": null,
"cdna_length": 1682,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MTRFR",
"gene_hgnc_id": 26784,
"hgvs_c": "c.347T>C",
"hgvs_p": "p.Val116Ala",
"transcript": "ENST00000543139.2",
"protein_id": "ENSP00000444843.2",
"transcript_support_level": 2,
"aa_start": 116,
"aa_end": null,
"aa_length": 166,
"cds_start": 347,
"cds_end": null,
"cds_length": 501,
"cdna_start": 3665,
"cdna_end": null,
"cdna_length": 3819,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MTRFR",
"gene_hgnc_id": 26784,
"hgvs_c": "c.347T>C",
"hgvs_p": "p.Val116Ala",
"transcript": "ENST00000679849.1",
"protein_id": "ENSP00000505808.1",
"transcript_support_level": null,
"aa_start": 116,
"aa_end": null,
"aa_length": 166,
"cds_start": 347,
"cds_end": null,
"cds_length": 501,
"cdna_start": 603,
"cdna_end": null,
"cdna_length": 1805,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MTRFR",
"gene_hgnc_id": 26784,
"hgvs_c": "c.347T>C",
"hgvs_p": "p.Val116Ala",
"transcript": "XM_011538980.4",
"protein_id": "XP_011537282.1",
"transcript_support_level": null,
"aa_start": 116,
"aa_end": null,
"aa_length": 166,
"cds_start": 347,
"cds_end": null,
"cds_length": 501,
"cdna_start": 459,
"cdna_end": null,
"cdna_length": 1542,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MTRFR",
"gene_hgnc_id": 26784,
"hgvs_c": "c.347T>C",
"hgvs_p": "p.Val116Ala",
"transcript": "XM_024449273.2",
"protein_id": "XP_024305041.1",
"transcript_support_level": null,
"aa_start": 116,
"aa_end": null,
"aa_length": 166,
"cds_start": 347,
"cds_end": null,
"cds_length": 501,
"cdna_start": 782,
"cdna_end": null,
"cdna_length": 1865,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MTRFR",
"gene_hgnc_id": 26784,
"hgvs_c": "c.347T>C",
"hgvs_p": "p.Val116Ala",
"transcript": "XM_047429877.1",
"protein_id": "XP_047285833.1",
"transcript_support_level": null,
"aa_start": 116,
"aa_end": null,
"aa_length": 166,
"cds_start": 347,
"cds_end": null,
"cds_length": 501,
"cdna_start": 844,
"cdna_end": null,
"cdna_length": 1927,
"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": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MTRFR",
"gene_hgnc_id": 26784,
"hgvs_c": "n.*1064T>C",
"hgvs_p": null,
"transcript": "ENST00000425637.3",
"protein_id": "ENSP00000506680.1",
"transcript_support_level": 2,
"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": 2648,
"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": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MTRFR",
"gene_hgnc_id": 26784,
"hgvs_c": "n.*230T>C",
"hgvs_p": null,
"transcript": "ENST00000538888.6",
"protein_id": "ENSP00000505059.1",
"transcript_support_level": 3,
"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": 1634,
"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": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MTRFR",
"gene_hgnc_id": 26784,
"hgvs_c": "n.*735T>C",
"hgvs_p": null,
"transcript": "ENST00000680325.1",
"protein_id": "ENSP00000505277.1",
"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": 2234,
"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": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MTRFR",
"gene_hgnc_id": 26784,
"hgvs_c": "n.*1064T>C",
"hgvs_p": null,
"transcript": "ENST00000425637.3",
"protein_id": "ENSP00000506680.1",
"transcript_support_level": 2,
"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": 2648,
"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": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MTRFR",
"gene_hgnc_id": 26784,
"hgvs_c": "n.*230T>C",
"hgvs_p": null,
"transcript": "ENST00000538888.6",
"protein_id": "ENSP00000505059.1",
"transcript_support_level": 3,
"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": 1634,
"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": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MTRFR",
"gene_hgnc_id": 26784,
"hgvs_c": "n.*735T>C",
"hgvs_p": null,
"transcript": "ENST00000680325.1",
"protein_id": "ENSP00000505277.1",
"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": 2234,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": 4,
"intron_rank_end": null,
"gene_symbol": "CDK2AP1",
"gene_hgnc_id": 14002,
"hgvs_c": "n.809+2166A>G",
"hgvs_p": null,
"transcript": "ENST00000541002.7",
"protein_id": null,
"transcript_support_level": 5,
"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": 1110,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "CDK2AP1",
"gene_hgnc_id": 14002,
"hgvs_c": "n.280+2166A>G",
"hgvs_p": null,
"transcript": "ENST00000543217.6",
"protein_id": null,
"transcript_support_level": 2,
"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": 793,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": 6,
"intron_rank_end": null,
"gene_symbol": "CDK2AP1",
"gene_hgnc_id": 14002,
"hgvs_c": "n.*955+3397A>G",
"hgvs_p": null,
"transcript": "ENST00000652466.1",
"protein_id": "ENSP00000498286.1",
"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": 3828,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "MTRFR",
"gene_hgnc_id": 26784,
"dbsnp": "rs374464556",
"frequency_reference_population": 0.000003718214,
"hom_count_reference_population": 0,
"allele_count_reference_population": 6,
"gnomad_exomes_af": 0.00000342071,
"gnomad_genomes_af": 0.00000657921,
"gnomad_exomes_ac": 5,
"gnomad_genomes_ac": 1,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.4847606420516968,
"computational_prediction_selected": "Uncertain_significance",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.316,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": 0.3552,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.18,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 7.993,
"phylop100way_prediction": "Pathogenic",
"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": 2,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2",
"acmg_by_gene": [
{
"score": 2,
"benign_score": 0,
"pathogenic_score": 2,
"criteria": [
"PM2"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000253233.6",
"gene_symbol": "MTRFR",
"hgnc_id": 26784,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.347T>C",
"hgvs_p": "p.Val116Ala"
},
{
"score": 2,
"benign_score": 0,
"pathogenic_score": 2,
"criteria": [
"PM2"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000543217.6",
"gene_symbol": "CDK2AP1",
"hgnc_id": 14002,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.280+2166A>G",
"hgvs_p": null
}
],
"clinvar_disease": "Combined oxidative phosphorylation defect type 7,Hereditary spastic paraplegia 55",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"phenotype_combined": "Combined oxidative phosphorylation defect type 7;Hereditary spastic paraplegia 55",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}