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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: 3-45541917-G-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=3&pos=45541917&ref=G&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "3",
"pos": 45541917,
"ref": "G",
"alt": "T",
"effect": "missense_variant",
"transcript": "ENST00000645846.2",
"consequences": [
{
"aa_ref": "E",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 21,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LARS2",
"gene_hgnc_id": 17095,
"hgvs_c": "c.2493G>T",
"hgvs_p": "p.Glu831Asp",
"transcript": "NM_015340.4",
"protein_id": "NP_056155.1",
"transcript_support_level": null,
"aa_start": 831,
"aa_end": null,
"aa_length": 903,
"cds_start": 2493,
"cds_end": null,
"cds_length": 2712,
"cdna_start": 2685,
"cdna_end": null,
"cdna_length": 4781,
"mane_select": "ENST00000645846.2",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "D",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 21,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LARS2",
"gene_hgnc_id": 17095,
"hgvs_c": "c.2493G>T",
"hgvs_p": "p.Glu831Asp",
"transcript": "ENST00000645846.2",
"protein_id": "ENSP00000495093.1",
"transcript_support_level": null,
"aa_start": 831,
"aa_end": null,
"aa_length": 903,
"cds_start": 2493,
"cds_end": null,
"cds_length": 2712,
"cdna_start": 2685,
"cdna_end": null,
"cdna_length": 4781,
"mane_select": "NM_015340.4",
"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": 22,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LARS2",
"gene_hgnc_id": 17095,
"hgvs_c": "n.*883G>T",
"hgvs_p": null,
"transcript": "ENST00000265537.8",
"protein_id": "ENSP00000265537.4",
"transcript_support_level": 1,
"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": 4169,
"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": 22,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LARS2",
"gene_hgnc_id": 17095,
"hgvs_c": "n.*883G>T",
"hgvs_p": null,
"transcript": "ENST00000265537.8",
"protein_id": "ENSP00000265537.4",
"transcript_support_level": 1,
"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": 4169,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 20,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LARS2",
"gene_hgnc_id": 17095,
"hgvs_c": "c.2493G>T",
"hgvs_p": "p.Glu831Asp",
"transcript": "NM_001368263.1",
"protein_id": "NP_001355192.1",
"transcript_support_level": null,
"aa_start": 831,
"aa_end": null,
"aa_length": 903,
"cds_start": 2493,
"cds_end": null,
"cds_length": 2712,
"cdna_start": 2619,
"cdna_end": null,
"cdna_length": 4715,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 21,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LARS2",
"gene_hgnc_id": 17095,
"hgvs_c": "c.2493G>T",
"hgvs_p": "p.Glu831Asp",
"transcript": "ENST00000642274.1",
"protein_id": "ENSP00000495707.1",
"transcript_support_level": null,
"aa_start": 831,
"aa_end": null,
"aa_length": 903,
"cds_start": 2493,
"cds_end": null,
"cds_length": 2712,
"cdna_start": 2851,
"cdna_end": null,
"cdna_length": 4139,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 20,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LARS2",
"gene_hgnc_id": 17095,
"hgvs_c": "c.2493G>T",
"hgvs_p": "p.Glu831Asp",
"transcript": "ENST00000650792.2",
"protein_id": "ENSP00000498867.1",
"transcript_support_level": null,
"aa_start": 831,
"aa_end": null,
"aa_length": 903,
"cds_start": 2493,
"cds_end": null,
"cds_length": 2712,
"cdna_start": 2634,
"cdna_end": null,
"cdna_length": 10049,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 19,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LARS2",
"gene_hgnc_id": 17095,
"hgvs_c": "c.2364G>T",
"hgvs_p": "p.Glu788Asp",
"transcript": "ENST00000414984.5",
"protein_id": "ENSP00000412893.1",
"transcript_support_level": 5,
"aa_start": 788,
"aa_end": null,
"aa_length": 860,
"cds_start": 2364,
"cds_end": null,
"cds_length": 2583,
"cdna_start": 2502,
"cdna_end": null,
"cdna_length": 2800,
"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": 1,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LARS2",
"gene_hgnc_id": 17095,
"hgvs_c": "n.324G>T",
"hgvs_p": null,
"transcript": "ENST00000474585.1",
"protein_id": null,
"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": 567,
"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": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LARS2",
"gene_hgnc_id": 17095,
"hgvs_c": "n.*275G>T",
"hgvs_p": null,
"transcript": "ENST00000485461.1",
"protein_id": "ENSP00000494606.1",
"transcript_support_level": 4,
"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": 580,
"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": 21,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LARS2",
"gene_hgnc_id": 17095,
"hgvs_c": "n.*783G>T",
"hgvs_p": null,
"transcript": "ENST00000651549.1",
"protein_id": "ENSP00000499002.1",
"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": 3409,
"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": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LARS2",
"gene_hgnc_id": 17095,
"hgvs_c": "n.*275G>T",
"hgvs_p": null,
"transcript": "ENST00000485461.1",
"protein_id": "ENSP00000494606.1",
"transcript_support_level": 4,
"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": 580,
"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": 21,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LARS2",
"gene_hgnc_id": 17095,
"hgvs_c": "n.*783G>T",
"hgvs_p": null,
"transcript": "ENST00000651549.1",
"protein_id": "ENSP00000499002.1",
"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": 3409,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"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": 21,
"intron_rank": 20,
"intron_rank_end": null,
"gene_symbol": "LARS2",
"gene_hgnc_id": 17095,
"hgvs_c": "c.2405-5434G>T",
"hgvs_p": null,
"transcript": "XM_017006042.2",
"protein_id": "XP_016861531.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 804,
"cds_start": -4,
"cds_end": null,
"cds_length": 2415,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 4653,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"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": 20,
"intron_rank": 19,
"intron_rank_end": null,
"gene_symbol": "LARS2",
"gene_hgnc_id": 17095,
"hgvs_c": "c.2405-5434G>T",
"hgvs_p": null,
"transcript": "XM_047447830.1",
"protein_id": "XP_047303786.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 804,
"cds_start": -4,
"cds_end": null,
"cds_length": 2415,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 4587,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"downstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LARS2",
"gene_hgnc_id": 17095,
"hgvs_c": "n.*2361G>T",
"hgvs_p": null,
"transcript": "ENST00000652135.1",
"protein_id": "ENSP00000499104.1",
"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": 2752,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "LARS2",
"gene_hgnc_id": 17095,
"dbsnp": "rs9827689",
"frequency_reference_population": 0.0021533433,
"hom_count_reference_population": 65,
"allele_count_reference_population": 3476,
"gnomad_exomes_af": 0.00121625,
"gnomad_genomes_af": 0.0111445,
"gnomad_exomes_ac": 1778,
"gnomad_genomes_ac": 1698,
"gnomad_exomes_homalt": 35,
"gnomad_genomes_homalt": 30,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.00266382098197937,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.016,
"revel_prediction": "Benign",
"alphamissense_score": 0.0995,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.69,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 0.267,
"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": -20,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6_Very_Strong,BS1,BS2",
"acmg_by_gene": [
{
"score": -20,
"benign_score": 20,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong",
"BS1",
"BS2"
],
"verdict": "Benign",
"transcript": "ENST00000645846.2",
"gene_symbol": "LARS2",
"hgnc_id": 17095,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.2493G>T",
"hgvs_p": "p.Glu831Asp"
}
],
"clinvar_disease": "LARS2-related disorder,Perrault syndrome 4,not provided,not specified",
"clinvar_classification": "Benign",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "B:10",
"phenotype_combined": "not provided|not specified|Perrault syndrome 4|LARS2-related disorder",
"pathogenicity_classification_combined": "Benign",
"custom_annotations": null
}
],
"message": null
}