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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: 12-12126705-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=12&pos=12126705&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "12",
"pos": 12126705,
"ref": "G",
"alt": "A",
"effect": "missense_variant",
"transcript": "ENST00000261349.9",
"consequences": [
{
"aa_ref": "S",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 20,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LRP6",
"gene_hgnc_id": 6698,
"hgvs_c": "c.4298C>T",
"hgvs_p": "p.Ser1433Leu",
"transcript": "NM_002336.3",
"protein_id": "NP_002327.2",
"transcript_support_level": null,
"aa_start": 1433,
"aa_end": null,
"aa_length": 1613,
"cds_start": 4298,
"cds_end": null,
"cds_length": 4842,
"cdna_start": 4607,
"cdna_end": null,
"cdna_length": 10252,
"mane_select": "ENST00000261349.9",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "L",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 20,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LRP6",
"gene_hgnc_id": 6698,
"hgvs_c": "c.4298C>T",
"hgvs_p": "p.Ser1433Leu",
"transcript": "ENST00000261349.9",
"protein_id": "ENSP00000261349.4",
"transcript_support_level": 1,
"aa_start": 1433,
"aa_end": null,
"aa_length": 1613,
"cds_start": 4298,
"cds_end": null,
"cds_length": 4842,
"cdna_start": 4607,
"cdna_end": null,
"cdna_length": 10252,
"mane_select": "NM_002336.3",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 20,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LRP6",
"gene_hgnc_id": 6698,
"hgvs_c": "c.4163C>T",
"hgvs_p": "p.Ser1388Leu",
"transcript": "ENST00000543091.1",
"protein_id": "ENSP00000442472.1",
"transcript_support_level": 1,
"aa_start": 1388,
"aa_end": null,
"aa_length": 1568,
"cds_start": 4163,
"cds_end": null,
"cds_length": 4707,
"cdna_start": 4197,
"cdna_end": null,
"cdna_length": 4774,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 19,
"exon_rank_end": null,
"exon_count": 24,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LRP6",
"gene_hgnc_id": 6698,
"hgvs_c": "n.3890C>T",
"hgvs_p": null,
"transcript": "ENST00000538239.5",
"protein_id": "ENSP00000445083.1",
"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": 7812,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 21,
"exon_rank_end": null,
"exon_count": 24,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LRP6",
"gene_hgnc_id": 6698,
"hgvs_c": "c.4391C>T",
"hgvs_p": "p.Ser1464Leu",
"transcript": "NM_001414244.1",
"protein_id": "NP_001401173.1",
"transcript_support_level": null,
"aa_start": 1464,
"aa_end": null,
"aa_length": 1644,
"cds_start": 4391,
"cds_end": null,
"cds_length": 4935,
"cdna_start": 4700,
"cdna_end": null,
"cdna_length": 5592,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 20,
"exon_rank_end": null,
"exon_count": 24,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LRP6",
"gene_hgnc_id": 6698,
"hgvs_c": "c.4298C>T",
"hgvs_p": "p.Ser1433Leu",
"transcript": "NM_001414245.1",
"protein_id": "NP_001401174.1",
"transcript_support_level": null,
"aa_start": 1433,
"aa_end": null,
"aa_length": 1613,
"cds_start": 4298,
"cds_end": null,
"cds_length": 4842,
"cdna_start": 4607,
"cdna_end": null,
"cdna_length": 5487,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 20,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LRP6",
"gene_hgnc_id": 6698,
"hgvs_c": "c.4163C>T",
"hgvs_p": "p.Ser1388Leu",
"transcript": "NM_001414246.1",
"protein_id": "NP_001401175.1",
"transcript_support_level": null,
"aa_start": 1388,
"aa_end": null,
"aa_length": 1568,
"cds_start": 4163,
"cds_end": null,
"cds_length": 4707,
"cdna_start": 4472,
"cdna_end": null,
"cdna_length": 5364,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 19,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LRP6",
"gene_hgnc_id": 6698,
"hgvs_c": "c.4100C>T",
"hgvs_p": "p.Ser1367Leu",
"transcript": "NM_001414247.1",
"protein_id": "NP_001401176.1",
"transcript_support_level": null,
"aa_start": 1367,
"aa_end": null,
"aa_length": 1547,
"cds_start": 4100,
"cds_end": null,
"cds_length": 4644,
"cdna_start": 4409,
"cdna_end": null,
"cdna_length": 5301,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 20,
"exon_rank_end": null,
"exon_count": 24,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LRP6",
"gene_hgnc_id": 6698,
"hgvs_c": "c.4298C>T",
"hgvs_p": "p.Ser1433Leu",
"transcript": "NM_001414248.1",
"protein_id": "NP_001401177.1",
"transcript_support_level": null,
"aa_start": 1433,
"aa_end": null,
"aa_length": 1545,
"cds_start": 4298,
"cds_end": null,
"cds_length": 4638,
"cdna_start": 4607,
"cdna_end": null,
"cdna_length": 5613,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 20,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LRP6",
"gene_hgnc_id": 6698,
"hgvs_c": "c.4298C>T",
"hgvs_p": "p.Ser1433Leu",
"transcript": "NM_001414249.1",
"protein_id": "NP_001401178.1",
"transcript_support_level": null,
"aa_start": 1433,
"aa_end": null,
"aa_length": 1527,
"cds_start": 4298,
"cds_end": null,
"cds_length": 4584,
"cdna_start": 4607,
"cdna_end": null,
"cdna_length": 4990,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 20,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LRP6",
"gene_hgnc_id": 6698,
"hgvs_c": "c.4298C>T",
"hgvs_p": "p.Ser1433Leu",
"transcript": "NM_001414250.1",
"protein_id": "NP_001401179.1",
"transcript_support_level": null,
"aa_start": 1433,
"aa_end": null,
"aa_length": 1519,
"cds_start": 4298,
"cds_end": null,
"cds_length": 4560,
"cdna_start": 4607,
"cdna_end": null,
"cdna_length": 5003,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LRP6",
"gene_hgnc_id": 6698,
"hgvs_c": "c.3935C>T",
"hgvs_p": "p.Ser1312Leu",
"transcript": "NM_001414251.1",
"protein_id": "NP_001401180.1",
"transcript_support_level": null,
"aa_start": 1312,
"aa_end": null,
"aa_length": 1492,
"cds_start": 3935,
"cds_end": null,
"cds_length": 4479,
"cdna_start": 4244,
"cdna_end": null,
"cdna_length": 5136,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 19,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LRP6",
"gene_hgnc_id": 6698,
"hgvs_c": "c.3845C>T",
"hgvs_p": "p.Ser1282Leu",
"transcript": "NM_001414252.1",
"protein_id": "NP_001401181.1",
"transcript_support_level": null,
"aa_start": 1282,
"aa_end": null,
"aa_length": 1462,
"cds_start": 3845,
"cds_end": null,
"cds_length": 4389,
"cdna_start": 4213,
"cdna_end": null,
"cdna_length": 5105,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 20,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LRP6",
"gene_hgnc_id": 6698,
"hgvs_c": "c.3845C>T",
"hgvs_p": "p.Ser1282Leu",
"transcript": "NM_001414253.1",
"protein_id": "NP_001401182.1",
"transcript_support_level": null,
"aa_start": 1282,
"aa_end": null,
"aa_length": 1462,
"cds_start": 3845,
"cds_end": null,
"cds_length": 4389,
"cdna_start": 4524,
"cdna_end": null,
"cdna_length": 5416,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 20,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LRP6",
"gene_hgnc_id": 6698,
"hgvs_c": "c.3845C>T",
"hgvs_p": "p.Ser1282Leu",
"transcript": "NM_001414254.1",
"protein_id": "NP_001401183.1",
"transcript_support_level": null,
"aa_start": 1282,
"aa_end": null,
"aa_length": 1462,
"cds_start": 3845,
"cds_end": null,
"cds_length": 4389,
"cdna_start": 4603,
"cdna_end": null,
"cdna_length": 5495,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LRP6",
"gene_hgnc_id": 6698,
"hgvs_c": "c.3791C>T",
"hgvs_p": "p.Ser1264Leu",
"transcript": "NM_001414255.1",
"protein_id": "NP_001401184.1",
"transcript_support_level": null,
"aa_start": 1264,
"aa_end": null,
"aa_length": 1444,
"cds_start": 3791,
"cds_end": null,
"cds_length": 4335,
"cdna_start": 4100,
"cdna_end": null,
"cdna_length": 4992,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LRP6",
"gene_hgnc_id": 6698,
"hgvs_c": "c.3494C>T",
"hgvs_p": "p.Ser1165Leu",
"transcript": "XM_047428844.1",
"protein_id": "XP_047284800.1",
"transcript_support_level": null,
"aa_start": 1165,
"aa_end": null,
"aa_length": 1345,
"cds_start": 3494,
"cds_end": null,
"cds_length": 4038,
"cdna_start": 4260,
"cdna_end": null,
"cdna_length": 9905,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 20,
"exon_rank_end": null,
"exon_count": 25,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LRP6",
"gene_hgnc_id": 6698,
"hgvs_c": "n.4607C>T",
"hgvs_p": null,
"transcript": "NR_182264.1",
"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": 8531,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 20,
"exon_rank_end": null,
"exon_count": 24,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LRP6",
"gene_hgnc_id": 6698,
"hgvs_c": "n.4607C>T",
"hgvs_p": null,
"transcript": "XR_002957325.2",
"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": 9213,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "LRP6",
"gene_hgnc_id": 6698,
"hgvs_c": "c.122-2043C>T",
"hgvs_p": null,
"transcript": "ENST00000540527.5",
"protein_id": "ENSP00000443239.1",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": 69,
"cds_start": -4,
"cds_end": null,
"cds_length": 210,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 593,
"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": 7,
"intron_rank": 4,
"intron_rank_end": null,
"gene_symbol": "BCL2L14",
"gene_hgnc_id": 16657,
"hgvs_c": "n.711+11378G>A",
"hgvs_p": null,
"transcript": "ENST00000298566.2",
"protein_id": "ENSP00000298566.1",
"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": 1247,
"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": 4,
"intron_rank": 3,
"intron_rank_end": null,
"gene_symbol": "LRP6",
"gene_hgnc_id": 6698,
"hgvs_c": "n.403-1273C>T",
"hgvs_p": null,
"transcript": "ENST00000540415.1",
"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": 473,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "LRP6",
"gene_hgnc_id": 6698,
"dbsnp": "rs869320647",
"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": 0.44014865159988403,
"computational_prediction_selected": "Uncertain_significance",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.05000000074505806,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.133,
"revel_prediction": "Benign",
"alphamissense_score": 0.1219,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.35,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 9.564,
"phylop100way_prediction": "Pathogenic",
"spliceai_max_score": 0.05,
"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": "ENST00000261349.9",
"gene_symbol": "LRP6",
"hgnc_id": 6698,
"effects": [
"missense_variant"
],
"inheritance_mode": "AD,Unknown",
"hgvs_c": "c.4298C>T",
"hgvs_p": "p.Ser1433Leu"
},
{
"score": 2,
"benign_score": 0,
"pathogenic_score": 2,
"criteria": [
"PM2"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000298566.2",
"gene_symbol": "BCL2L14",
"hgnc_id": 16657,
"effects": [
"intron_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "n.711+11378G>A",
"hgvs_p": null
}
],
"clinvar_disease": "Orofacial cleft,Tooth agenesis",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"phenotype_combined": "Orofacial cleft;Tooth agenesis",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}