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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: 3-8548722-T-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=3&pos=8548722&ref=T&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "3",
"pos": 8548722,
"ref": "T",
"alt": "A",
"effect": "missense_variant",
"transcript": "NM_014583.4",
"consequences": [
{
"aa_ref": "L",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LMCD1",
"gene_hgnc_id": 6633,
"hgvs_c": "c.542T>A",
"hgvs_p": "p.Leu181Gln",
"transcript": "NM_014583.4",
"protein_id": "NP_055398.1",
"transcript_support_level": null,
"aa_start": 181,
"aa_end": null,
"aa_length": 365,
"cds_start": 542,
"cds_end": null,
"cds_length": 1098,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000157600.8",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_014583.4"
},
{
"aa_ref": "L",
"aa_alt": "Q",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LMCD1",
"gene_hgnc_id": 6633,
"hgvs_c": "c.542T>A",
"hgvs_p": "p.Leu181Gln",
"transcript": "ENST00000157600.8",
"protein_id": "ENSP00000157600.3",
"transcript_support_level": 1,
"aa_start": 181,
"aa_end": null,
"aa_length": 365,
"cds_start": 542,
"cds_end": null,
"cds_length": 1098,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_014583.4",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000157600.8"
},
{
"aa_ref": "L",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LMCD1",
"gene_hgnc_id": 6633,
"hgvs_c": "c.533T>A",
"hgvs_p": "p.Leu178Gln",
"transcript": "ENST00000880274.1",
"protein_id": "ENSP00000550333.1",
"transcript_support_level": null,
"aa_start": 178,
"aa_end": null,
"aa_length": 362,
"cds_start": 533,
"cds_end": null,
"cds_length": 1089,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000880274.1"
},
{
"aa_ref": "L",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LMCD1",
"gene_hgnc_id": 6633,
"hgvs_c": "c.542T>A",
"hgvs_p": "p.Leu181Gln",
"transcript": "ENST00000957327.1",
"protein_id": "ENSP00000627386.1",
"transcript_support_level": null,
"aa_start": 181,
"aa_end": null,
"aa_length": 293,
"cds_start": 542,
"cds_end": null,
"cds_length": 882,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000957327.1"
},
{
"aa_ref": "L",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LMCD1",
"gene_hgnc_id": 6633,
"hgvs_c": "c.323T>A",
"hgvs_p": "p.Leu108Gln",
"transcript": "NM_001278233.2",
"protein_id": "NP_001265162.1",
"transcript_support_level": null,
"aa_start": 108,
"aa_end": null,
"aa_length": 292,
"cds_start": 323,
"cds_end": null,
"cds_length": 879,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001278233.2"
},
{
"aa_ref": "L",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LMCD1",
"gene_hgnc_id": 6633,
"hgvs_c": "c.323T>A",
"hgvs_p": "p.Leu108Gln",
"transcript": "ENST00000454244.4",
"protein_id": "ENSP00000396515.1",
"transcript_support_level": 2,
"aa_start": 108,
"aa_end": null,
"aa_length": 292,
"cds_start": 323,
"cds_end": null,
"cds_length": 879,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000454244.4"
},
{
"aa_ref": "L",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LMCD1",
"gene_hgnc_id": 6633,
"hgvs_c": "c.206T>A",
"hgvs_p": "p.Leu69Gln",
"transcript": "NM_001278234.2",
"protein_id": "NP_001265163.1",
"transcript_support_level": null,
"aa_start": 69,
"aa_end": null,
"aa_length": 253,
"cds_start": 206,
"cds_end": null,
"cds_length": 762,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001278234.2"
},
{
"aa_ref": "L",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LMCD1",
"gene_hgnc_id": 6633,
"hgvs_c": "c.206T>A",
"hgvs_p": "p.Leu69Gln",
"transcript": "ENST00000397386.7",
"protein_id": "ENSP00000380542.3",
"transcript_support_level": 2,
"aa_start": 69,
"aa_end": null,
"aa_length": 253,
"cds_start": 206,
"cds_end": null,
"cds_length": 762,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000397386.7"
},
{
"aa_ref": "L",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LMCD1",
"gene_hgnc_id": 6633,
"hgvs_c": "c.197T>A",
"hgvs_p": "p.Leu66Gln",
"transcript": "ENST00000921338.1",
"protein_id": "ENSP00000591397.1",
"transcript_support_level": null,
"aa_start": 66,
"aa_end": null,
"aa_length": 250,
"cds_start": 197,
"cds_end": null,
"cds_length": 753,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000921338.1"
},
{
"aa_ref": "L",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LMCD1",
"gene_hgnc_id": 6633,
"hgvs_c": "c.542T>A",
"hgvs_p": "p.Leu181Gln",
"transcript": "NM_001278235.2",
"protein_id": "NP_001265164.1",
"transcript_support_level": null,
"aa_start": 181,
"aa_end": null,
"aa_length": 247,
"cds_start": 542,
"cds_end": null,
"cds_length": 744,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001278235.2"
},
{
"aa_ref": "L",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LMCD1",
"gene_hgnc_id": 6633,
"hgvs_c": "c.542T>A",
"hgvs_p": "p.Leu181Gln",
"transcript": "ENST00000426878.2",
"protein_id": "ENSP00000411222.2",
"transcript_support_level": 2,
"aa_start": 181,
"aa_end": null,
"aa_length": 247,
"cds_start": 542,
"cds_end": null,
"cds_length": 744,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000426878.2"
},
{
"aa_ref": "L",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LMCD1",
"gene_hgnc_id": 6633,
"hgvs_c": "c.560T>A",
"hgvs_p": "p.Leu187Gln",
"transcript": "ENST00000415597.5",
"protein_id": "ENSP00000400555.1",
"transcript_support_level": 5,
"aa_start": 187,
"aa_end": null,
"aa_length": 232,
"cds_start": 560,
"cds_end": null,
"cds_length": 701,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000415597.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": 3,
"intron_rank_end": null,
"gene_symbol": "LMCD1",
"gene_hgnc_id": 6633,
"hgvs_c": "c.387+11282T>A",
"hgvs_p": null,
"transcript": "ENST00000957328.1",
"protein_id": "ENSP00000627387.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 253,
"cds_start": null,
"cds_end": null,
"cds_length": 762,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000957328.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "LMCD1",
"gene_hgnc_id": 6633,
"hgvs_c": "c.43-16710T>A",
"hgvs_p": null,
"transcript": "ENST00000957329.1",
"protein_id": "ENSP00000627388.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 138,
"cds_start": null,
"cds_end": null,
"cds_length": 417,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000957329.1"
},
{
"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": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LMCD1",
"gene_hgnc_id": 6633,
"hgvs_c": "n.*109T>A",
"hgvs_p": null,
"transcript": "ENST00000456506.2",
"protein_id": "ENSP00000405049.1",
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "nonsense_mediated_decay",
"feature": "ENST00000456506.2"
},
{
"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": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LMCD1",
"gene_hgnc_id": 6633,
"hgvs_c": "n.*109T>A",
"hgvs_p": null,
"transcript": "ENST00000456506.2",
"protein_id": "ENSP00000405049.1",
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "nonsense_mediated_decay",
"feature": "ENST00000456506.2"
},
{
"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": 4,
"intron_rank": 3,
"intron_rank_end": null,
"gene_symbol": "LMCD1-AS1",
"gene_hgnc_id": 44477,
"hgvs_c": "n.336-49873A>T",
"hgvs_p": null,
"transcript": "ENST00000439407.1",
"protein_id": null,
"transcript_support_level": 4,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "ENST00000439407.1"
}
],
"gene_symbol": "LMCD1",
"gene_hgnc_id": 6633,
"dbsnp": null,
"frequency_reference_population": null,
"hom_count_reference_population": 0,
"allele_count_reference_population": 0,
"gnomad_exomes_af": null,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": null,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": null,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.09550720453262329,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.21,
"revel_prediction": "Benign",
"alphamissense_score": 0.0712,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.29,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 0.376,
"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": 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_014583.4",
"gene_symbol": "LMCD1",
"hgnc_id": 6633,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.542T>A",
"hgvs_p": "p.Leu181Gln"
},
{
"score": 0,
"benign_score": 2,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4_Moderate"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000439407.1",
"gene_symbol": "LMCD1-AS1",
"hgnc_id": 44477,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.336-49873A>T",
"hgvs_p": null
}
],
"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
}