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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: 11-558713-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=11&pos=558713&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 4,
"criteria": [
"BP4_Strong"
],
"effects": [
"missense_variant"
],
"gene_symbol": "LMNTD2",
"hgnc_id": 28561,
"hgvs_c": "c.212G>A",
"hgvs_p": "p.Arg71Gln",
"inheritance_mode": "AR",
"pathogenic_score": 0,
"score": -4,
"transcript": "NM_173573.3",
"verdict": "Likely_benign"
},
{
"benign_score": 4,
"criteria": [
"BP4_Strong"
],
"effects": [
"non_coding_transcript_exon_variant"
],
"gene_symbol": "LMNTD2-AS1",
"hgnc_id": 41204,
"hgvs_c": "n.1119C>T",
"hgvs_p": null,
"inheritance_mode": "",
"pathogenic_score": 0,
"score": -4,
"transcript": "ENST00000527620.5",
"verdict": "Likely_benign"
}
],
"acmg_classification": "Likely_benign",
"acmg_criteria": "BP4_Strong",
"acmg_score": -4,
"allele_count_reference_population": 49,
"alphamissense_prediction": null,
"alphamissense_score": 0.2381,
"alt": "T",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Benign",
"bayesdelnoaf_score": -0.44,
"chr": "11",
"clinvar_classification": "",
"clinvar_disease": "",
"clinvar_review_status": "",
"clinvar_submissions_summary": "",
"computational_prediction_selected": "Benign",
"computational_score_selected": 0.036952316761016846,
"computational_source_selected": "MetaRNN",
"consequences": [
{
"aa_alt": "Q",
"aa_end": null,
"aa_length": 634,
"aa_ref": "R",
"aa_start": 71,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2057,
"cdna_start": 234,
"cds_end": null,
"cds_length": 1905,
"cds_start": 212,
"consequences": [
"missense_variant"
],
"exon_count": 14,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "NM_173573.3",
"gene_hgnc_id": 28561,
"gene_symbol": "LMNTD2",
"hgvs_c": "c.212G>A",
"hgvs_p": "p.Arg71Gln",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000329451.8",
"protein_coding": true,
"protein_id": "NP_775844.2",
"strand": false,
"transcript": "NM_173573.3",
"transcript_support_level": null
},
{
"aa_alt": "Q",
"aa_end": null,
"aa_length": 634,
"aa_ref": "R",
"aa_start": 71,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 2057,
"cdna_start": 234,
"cds_end": null,
"cds_length": 1905,
"cds_start": 212,
"consequences": [
"missense_variant"
],
"exon_count": 14,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "ENST00000329451.8",
"gene_hgnc_id": 28561,
"gene_symbol": "LMNTD2",
"hgvs_c": "c.212G>A",
"hgvs_p": "p.Arg71Gln",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_173573.3",
"protein_coding": true,
"protein_id": "ENSP00000331167.3",
"strand": false,
"transcript": "ENST00000329451.8",
"transcript_support_level": 1
},
{
"aa_alt": "Q",
"aa_end": null,
"aa_length": 639,
"aa_ref": "R",
"aa_start": 71,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2071,
"cdna_start": 234,
"cds_end": null,
"cds_length": 1920,
"cds_start": 212,
"consequences": [
"missense_variant"
],
"exon_count": 14,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "ENST00000886189.1",
"gene_hgnc_id": 28561,
"gene_symbol": "LMNTD2",
"hgvs_c": "c.212G>A",
"hgvs_p": "p.Arg71Gln",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000556248.1",
"strand": false,
"transcript": "ENST00000886189.1",
"transcript_support_level": null
},
{
"aa_alt": "Q",
"aa_end": null,
"aa_length": 621,
"aa_ref": "R",
"aa_start": 77,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1994,
"cdna_start": 234,
"cds_end": null,
"cds_length": 1866,
"cds_start": 230,
"consequences": [
"missense_variant"
],
"exon_count": 14,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "ENST00000886190.1",
"gene_hgnc_id": 28561,
"gene_symbol": "LMNTD2",
"hgvs_c": "c.230G>A",
"hgvs_p": "p.Arg77Gln",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000556249.1",
"strand": false,
"transcript": "ENST00000886190.1",
"transcript_support_level": null
},
{
"aa_alt": "Q",
"aa_end": null,
"aa_length": 301,
"aa_ref": "R",
"aa_start": 78,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1051,
"cdna_start": 378,
"cds_end": null,
"cds_length": 906,
"cds_start": 233,
"consequences": [
"missense_variant"
],
"exon_count": 9,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "ENST00000441853.5",
"gene_hgnc_id": 28561,
"gene_symbol": "LMNTD2",
"hgvs_c": "c.233G>A",
"hgvs_p": "p.Arg78Gln",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000393529.1",
"strand": false,
"transcript": "ENST00000441853.5",
"transcript_support_level": 3
},
{
"aa_alt": "Q",
"aa_end": null,
"aa_length": 246,
"aa_ref": "R",
"aa_start": 81,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 798,
"cdna_start": 297,
"cds_end": null,
"cds_length": 743,
"cds_start": 242,
"consequences": [
"missense_variant"
],
"exon_count": 7,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "ENST00000486629.1",
"gene_hgnc_id": 28561,
"gene_symbol": "LMNTD2",
"hgvs_c": "c.242G>A",
"hgvs_p": "p.Arg81Gln",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000435529.1",
"strand": false,
"transcript": "ENST00000486629.1",
"transcript_support_level": 5
},
{
"aa_alt": "Q",
"aa_end": null,
"aa_length": 707,
"aa_ref": "R",
"aa_start": 139,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3408,
"cdna_start": 1570,
"cds_end": null,
"cds_length": 2124,
"cds_start": 416,
"consequences": [
"missense_variant"
],
"exon_count": 14,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "XM_011519965.3",
"gene_hgnc_id": 28561,
"gene_symbol": "LMNTD2",
"hgvs_c": "c.416G>A",
"hgvs_p": "p.Arg139Gln",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_011518267.2",
"strand": false,
"transcript": "XM_011519965.3",
"transcript_support_level": null
},
{
"aa_alt": "Q",
"aa_end": null,
"aa_length": 702,
"aa_ref": "R",
"aa_start": 139,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3393,
"cdna_start": 1570,
"cds_end": null,
"cds_length": 2109,
"cds_start": 416,
"consequences": [
"missense_variant"
],
"exon_count": 14,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "XM_047426712.1",
"gene_hgnc_id": 28561,
"gene_symbol": "LMNTD2",
"hgvs_c": "c.416G>A",
"hgvs_p": "p.Arg139Gln",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_047282668.1",
"strand": false,
"transcript": "XM_047426712.1",
"transcript_support_level": null
},
{
"aa_alt": "Q",
"aa_end": null,
"aa_length": 667,
"aa_ref": "R",
"aa_start": 139,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3288,
"cdna_start": 1570,
"cds_end": null,
"cds_length": 2004,
"cds_start": 416,
"consequences": [
"missense_variant"
],
"exon_count": 13,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "XM_011519967.3",
"gene_hgnc_id": 28561,
"gene_symbol": "LMNTD2",
"hgvs_c": "c.416G>A",
"hgvs_p": "p.Arg139Gln",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_011518269.2",
"strand": false,
"transcript": "XM_011519967.3",
"transcript_support_level": null
},
{
"aa_alt": "Q",
"aa_end": null,
"aa_length": 639,
"aa_ref": "R",
"aa_start": 71,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2072,
"cdna_start": 234,
"cds_end": null,
"cds_length": 1920,
"cds_start": 212,
"consequences": [
"missense_variant"
],
"exon_count": 14,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "XM_047426713.1",
"gene_hgnc_id": 28561,
"gene_symbol": "LMNTD2",
"hgvs_c": "c.212G>A",
"hgvs_p": "p.Arg71Gln",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_047282669.1",
"strand": false,
"transcript": "XM_047426713.1",
"transcript_support_level": null
},
{
"aa_alt": "Q",
"aa_end": null,
"aa_length": 630,
"aa_ref": "R",
"aa_start": 139,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3126,
"cdna_start": 1570,
"cds_end": null,
"cds_length": 1893,
"cds_start": 416,
"consequences": [
"missense_variant"
],
"exon_count": 13,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "XM_017017479.3",
"gene_hgnc_id": 28561,
"gene_symbol": "LMNTD2",
"hgvs_c": "c.416G>A",
"hgvs_p": "p.Arg139Gln",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_016872968.1",
"strand": false,
"transcript": "XM_017017479.3",
"transcript_support_level": null
},
{
"aa_alt": "Q",
"aa_end": null,
"aa_length": 406,
"aa_ref": "R",
"aa_start": 139,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2471,
"cdna_start": 1570,
"cds_end": null,
"cds_length": 1221,
"cds_start": 416,
"consequences": [
"missense_variant"
],
"exon_count": 10,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "XM_047426714.1",
"gene_hgnc_id": 28561,
"gene_symbol": "LMNTD2",
"hgvs_c": "c.416G>A",
"hgvs_p": "p.Arg139Gln",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_047282670.1",
"strand": false,
"transcript": "XM_047426714.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "retained_intron",
"canonical": false,
"cdna_end": null,
"cdna_length": 608,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 3,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "ENST00000492515.1",
"gene_hgnc_id": 28561,
"gene_symbol": "LMNTD2",
"hgvs_c": "n.371G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": false,
"transcript": "ENST00000492515.1",
"transcript_support_level": 4
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 2210,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 2,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "ENST00000527620.5",
"gene_hgnc_id": 41204,
"gene_symbol": "LMNTD2-AS1",
"hgvs_c": "n.1119C>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": true,
"transcript": "ENST00000527620.5",
"transcript_support_level": 2
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 530,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"upstream_gene_variant"
],
"exon_count": 3,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000527113.2",
"gene_hgnc_id": 41204,
"gene_symbol": "LMNTD2-AS1",
"hgvs_c": "n.-179C>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": true,
"transcript": "ENST00000527113.2",
"transcript_support_level": 4
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs148047813",
"effect": "missense_variant",
"frequency_reference_population": 0.000030496534,
"gene_hgnc_id": 28561,
"gene_symbol": "LMNTD2",
"gnomad_exomes_ac": 38,
"gnomad_exomes_af": 0.0000261284,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_ac": 11,
"gnomad_genomes_af": 0.0000721861,
"gnomad_genomes_homalt": 0,
"gnomad_mito_heteroplasmic": null,
"gnomad_mito_homoplasmic": null,
"hom_count_reference_population": 0,
"mitotip_prediction": null,
"mitotip_score": null,
"pathogenicity_classification_combined": null,
"phenotype_combined": null,
"phylop100way_prediction": "Benign",
"phylop100way_score": -0.363,
"pos": 558713,
"ref": "C",
"revel_prediction": "Benign",
"revel_score": 0.066,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0,
"transcript": "NM_173573.3"
}
]
}