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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: 2-43774140-T-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=2&pos=43774140&ref=T&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "2",
"pos": 43774140,
"ref": "T",
"alt": "C",
"effect": "start_lost",
"transcript": "ENST00000260605.12",
"consequences": [
{
"aa_ref": "M",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"start_lost"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DYNC2LI1",
"gene_hgnc_id": 24595,
"hgvs_c": "c.2T>C",
"hgvs_p": "p.Met1?",
"transcript": "NM_016008.4",
"protein_id": "NP_057092.2",
"transcript_support_level": null,
"aa_start": 1,
"aa_end": null,
"aa_length": 351,
"cds_start": 2,
"cds_end": null,
"cds_length": 1056,
"cdna_start": 102,
"cdna_end": null,
"cdna_length": 1399,
"mane_select": "ENST00000260605.12",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "M",
"aa_alt": "T",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"start_lost"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DYNC2LI1",
"gene_hgnc_id": 24595,
"hgvs_c": "c.2T>C",
"hgvs_p": "p.Met1?",
"transcript": "ENST00000260605.12",
"protein_id": "ENSP00000260605.8",
"transcript_support_level": 1,
"aa_start": 1,
"aa_end": null,
"aa_length": 351,
"cds_start": 2,
"cds_end": null,
"cds_length": 1056,
"cdna_start": 102,
"cdna_end": null,
"cdna_length": 1399,
"mane_select": "NM_016008.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "M",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"start_lost"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DYNC2LI1",
"gene_hgnc_id": 24595,
"hgvs_c": "c.2T>C",
"hgvs_p": "p.Met1?",
"transcript": "ENST00000605786.5",
"protein_id": "ENSP00000474032.1",
"transcript_support_level": 1,
"aa_start": 1,
"aa_end": null,
"aa_length": 352,
"cds_start": 2,
"cds_end": null,
"cds_length": 1059,
"cdna_start": 59,
"cdna_end": null,
"cdna_length": 1346,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "M",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"start_lost"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DYNC2LI1",
"gene_hgnc_id": 24595,
"hgvs_c": "c.2T>C",
"hgvs_p": "p.Met1?",
"transcript": "ENST00000406852.7",
"protein_id": "ENSP00000385738.3",
"transcript_support_level": 1,
"aa_start": 1,
"aa_end": null,
"aa_length": 201,
"cds_start": 2,
"cds_end": null,
"cds_length": 606,
"cdna_start": 92,
"cdna_end": null,
"cdna_length": 1133,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "M",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"start_lost"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DYNC2LI1",
"gene_hgnc_id": 24595,
"hgvs_c": "c.2T>C",
"hgvs_p": "p.Met1?",
"transcript": "ENST00000398823.6",
"protein_id": "ENSP00000381804.2",
"transcript_support_level": 1,
"aa_start": 1,
"aa_end": null,
"aa_length": 144,
"cds_start": 2,
"cds_end": null,
"cds_length": 435,
"cdna_start": 77,
"cdna_end": null,
"cdna_length": 2903,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "M",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"start_lost"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DYNC2LI1",
"gene_hgnc_id": 24595,
"hgvs_c": "c.2T>C",
"hgvs_p": "p.Met1?",
"transcript": "NM_001348913.2",
"protein_id": "NP_001335842.1",
"transcript_support_level": null,
"aa_start": 1,
"aa_end": null,
"aa_length": 374,
"cds_start": 2,
"cds_end": null,
"cds_length": 1125,
"cdna_start": 102,
"cdna_end": null,
"cdna_length": 2202,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "M",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"start_lost"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DYNC2LI1",
"gene_hgnc_id": 24595,
"hgvs_c": "c.2T>C",
"hgvs_p": "p.Met1?",
"transcript": "NM_001348912.2",
"protein_id": "NP_001335841.1",
"transcript_support_level": null,
"aa_start": 1,
"aa_end": null,
"aa_length": 373,
"cds_start": 2,
"cds_end": null,
"cds_length": 1122,
"cdna_start": 102,
"cdna_end": null,
"cdna_length": 2199,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "M",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"start_lost"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DYNC2LI1",
"gene_hgnc_id": 24595,
"hgvs_c": "c.2T>C",
"hgvs_p": "p.Met1?",
"transcript": "NM_001193464.2",
"protein_id": "NP_001180393.1",
"transcript_support_level": null,
"aa_start": 1,
"aa_end": null,
"aa_length": 352,
"cds_start": 2,
"cds_end": null,
"cds_length": 1059,
"cdna_start": 102,
"cdna_end": null,
"cdna_length": 1402,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "M",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"start_lost"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DYNC2LI1",
"gene_hgnc_id": 24595,
"hgvs_c": "c.2T>C",
"hgvs_p": "p.Met1?",
"transcript": "NM_015522.4",
"protein_id": "NP_056337.1",
"transcript_support_level": null,
"aa_start": 1,
"aa_end": null,
"aa_length": 201,
"cds_start": 2,
"cds_end": null,
"cds_length": 606,
"cdna_start": 102,
"cdna_end": null,
"cdna_length": 1143,
"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": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DYNC2LI1",
"gene_hgnc_id": 24595,
"hgvs_c": "n.2T>C",
"hgvs_p": null,
"transcript": "ENST00000462426.1",
"protein_id": "ENSP00000428082.1",
"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": 713,
"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": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DYNC2LI1",
"gene_hgnc_id": 24595,
"hgvs_c": "n.2T>C",
"hgvs_p": null,
"transcript": "ENST00000479242.5",
"protein_id": "ENSP00000430525.1",
"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": 568,
"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": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DYNC2LI1",
"gene_hgnc_id": 24595,
"hgvs_c": "n.77T>C",
"hgvs_p": null,
"transcript": "ENST00000489222.6",
"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": 687,
"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": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DYNC2LI1",
"gene_hgnc_id": 24595,
"hgvs_c": "n.2T>C",
"hgvs_p": null,
"transcript": "ENST00000496980.6",
"protein_id": "ENSP00000430356.1",
"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": 547,
"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": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LOC105374571",
"gene_hgnc_id": null,
"hgvs_c": "n.-13T>C",
"hgvs_p": null,
"transcript": "XR_940033.2",
"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": 514,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "DYNC2LI1",
"gene_hgnc_id": 24595,
"dbsnp": "rs200859699",
"frequency_reference_population": 0.000022924269,
"hom_count_reference_population": 0,
"allele_count_reference_population": 37,
"gnomad_exomes_af": 0.0000232606,
"gnomad_genomes_af": 0.0000196964,
"gnomad_exomes_ac": 34,
"gnomad_genomes_ac": 3,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.7181569337844849,
"computational_prediction_selected": "Uncertain_significance",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.286,
"revel_prediction": "Benign",
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.09,
"bayesdelnoaf_prediction": "Uncertain_significance",
"phylop100way_score": 3.093,
"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": 8,
"acmg_classification": "Likely_pathogenic",
"acmg_criteria": "PVS1_Strong,PM2,PP5_Moderate",
"acmg_by_gene": [
{
"score": 8,
"benign_score": 0,
"pathogenic_score": 8,
"criteria": [
"PVS1_Strong",
"PM2",
"PP5_Moderate"
],
"verdict": "Likely_pathogenic",
"transcript": "ENST00000260605.12",
"gene_symbol": "DYNC2LI1",
"hgnc_id": 24595,
"effects": [
"start_lost"
],
"inheritance_mode": "AR",
"hgvs_c": "c.2T>C",
"hgvs_p": "p.Met1?"
},
{
"score": 4,
"benign_score": 0,
"pathogenic_score": 4,
"criteria": [
"PM2",
"PP5_Moderate"
],
"verdict": "Uncertain_significance",
"transcript": "XR_940033.2",
"gene_symbol": "LOC105374571",
"hgnc_id": null,
"effects": [
"upstream_gene_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.-13T>C",
"hgvs_p": null
}
],
"clinvar_disease": "Short-rib thoracic dysplasia 15 with polydactyly,not provided",
"clinvar_classification": "Pathogenic",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "P:1",
"phenotype_combined": "Short-rib thoracic dysplasia 15 with polydactyly|not provided",
"pathogenicity_classification_combined": "Pathogenic",
"custom_annotations": null
}
],
"message": null
}