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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: 6-129492013-C-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=6&pos=129492013&ref=C&alt=A&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 4,
"criteria": [
"BP4_Strong"
],
"effects": [
"missense_variant"
],
"gene_symbol": "LAMA2",
"hgnc_id": 6482,
"hgvs_c": "c.8011C>A",
"hgvs_p": "p.Pro2671Thr",
"inheritance_mode": "AR",
"pathogenic_score": 0,
"score": -4,
"transcript": "NM_000426.4",
"verdict": "Likely_benign"
},
{
"benign_score": 4,
"criteria": [
"BP4_Strong"
],
"effects": [
"non_coding_transcript_exon_variant"
],
"gene_symbol": "ENSG00000226149",
"hgnc_id": null,
"hgvs_c": "n.3273G>T",
"hgvs_p": null,
"inheritance_mode": "",
"pathogenic_score": 0,
"score": -4,
"transcript": "ENST00000657779.1",
"verdict": "Likely_benign"
}
],
"acmg_classification": "Likely_benign",
"acmg_criteria": "BP4_Strong",
"acmg_score": -4,
"allele_count_reference_population": 80,
"alphamissense_prediction": null,
"alphamissense_score": 0.1082,
"alt": "A",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Benign",
"bayesdelnoaf_score": -0.42,
"chr": "6",
"clinvar_classification": "Conflicting classifications of pathogenicity",
"clinvar_disease": " autosomal recessive 23, limb-girdle,Congenital muscular dystrophy due to partial LAMA2 deficiency,LAMA2-related muscular dystrophy,Merosin deficient congenital muscular dystrophy,Muscular dystrophy,not provided,not specified",
"clinvar_review_status": "criteria provided, conflicting classifications",
"clinvar_submissions_summary": "US:4 B:1",
"computational_prediction_selected": "Benign",
"computational_score_selected": 0.007295399904251099,
"computational_source_selected": "MetaRNN",
"consequences": [
{
"aa_alt": "T",
"aa_end": null,
"aa_length": 3122,
"aa_ref": "P",
"aa_start": 2671,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 9696,
"cdna_start": 8119,
"cds_end": null,
"cds_length": 9369,
"cds_start": 8011,
"consequences": [
"missense_variant"
],
"exon_count": 65,
"exon_rank": 57,
"exon_rank_end": null,
"feature": "NM_000426.4",
"gene_hgnc_id": 6482,
"gene_symbol": "LAMA2",
"hgvs_c": "c.8011C>A",
"hgvs_p": "p.Pro2671Thr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000421865.3",
"protein_coding": true,
"protein_id": "NP_000417.3",
"strand": true,
"transcript": "NM_000426.4",
"transcript_support_level": null
},
{
"aa_alt": "T",
"aa_end": null,
"aa_length": 3122,
"aa_ref": "P",
"aa_start": 2671,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 9696,
"cdna_start": 8119,
"cds_end": null,
"cds_length": 9369,
"cds_start": 8011,
"consequences": [
"missense_variant"
],
"exon_count": 65,
"exon_rank": 57,
"exon_rank_end": null,
"feature": "ENST00000421865.3",
"gene_hgnc_id": 6482,
"gene_symbol": "LAMA2",
"hgvs_c": "c.8011C>A",
"hgvs_p": "p.Pro2671Thr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_000426.4",
"protein_coding": true,
"protein_id": "ENSP00000400365.2",
"strand": true,
"transcript": "ENST00000421865.3",
"transcript_support_level": 5
},
{
"aa_alt": "T",
"aa_end": null,
"aa_length": 3210,
"aa_ref": "P",
"aa_start": 2759,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 9960,
"cdna_start": 8383,
"cds_end": null,
"cds_length": 9633,
"cds_start": 8275,
"consequences": [
"missense_variant"
],
"exon_count": 66,
"exon_rank": 58,
"exon_rank_end": null,
"feature": "ENST00000618192.5",
"gene_hgnc_id": 6482,
"gene_symbol": "LAMA2",
"hgvs_c": "c.8275C>A",
"hgvs_p": "p.Pro2759Thr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000480802.2",
"strand": true,
"transcript": "ENST00000618192.5",
"transcript_support_level": 5
},
{
"aa_alt": "T",
"aa_end": null,
"aa_length": 3118,
"aa_ref": "P",
"aa_start": 2667,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 9684,
"cdna_start": 8107,
"cds_end": null,
"cds_length": 9357,
"cds_start": 7999,
"consequences": [
"missense_variant"
],
"exon_count": 64,
"exon_rank": 56,
"exon_rank_end": null,
"feature": "NM_001079823.2",
"gene_hgnc_id": 6482,
"gene_symbol": "LAMA2",
"hgvs_c": "c.7999C>A",
"hgvs_p": "p.Pro2667Thr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001073291.2",
"strand": true,
"transcript": "NM_001079823.2",
"transcript_support_level": null
},
{
"aa_alt": "T",
"aa_end": null,
"aa_length": 3118,
"aa_ref": "P",
"aa_start": 2667,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 9656,
"cdna_start": 8107,
"cds_end": null,
"cds_length": 9357,
"cds_start": 7999,
"consequences": [
"missense_variant"
],
"exon_count": 64,
"exon_rank": 56,
"exon_rank_end": null,
"feature": "ENST00000617695.5",
"gene_hgnc_id": 6482,
"gene_symbol": "LAMA2",
"hgvs_c": "c.7999C>A",
"hgvs_p": "p.Pro2667Thr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000481744.2",
"strand": true,
"transcript": "ENST00000617695.5",
"transcript_support_level": 5
},
{
"aa_alt": "T",
"aa_end": null,
"aa_length": 477,
"aa_ref": "P",
"aa_start": 26,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2015,
"cdna_start": 476,
"cds_end": null,
"cds_length": 1434,
"cds_start": 76,
"consequences": [
"missense_variant"
],
"exon_count": 10,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000494137.2",
"gene_hgnc_id": 6482,
"gene_symbol": "LAMA2",
"hgvs_c": "c.76C>A",
"hgvs_p": "p.Pro26Thr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000510626.1",
"strand": true,
"transcript": "ENST00000494137.2",
"transcript_support_level": 3
},
{
"aa_alt": "T",
"aa_end": null,
"aa_length": 477,
"aa_ref": "P",
"aa_start": 26,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1901,
"cdna_start": 324,
"cds_end": null,
"cds_length": 1434,
"cds_start": 76,
"consequences": [
"missense_variant"
],
"exon_count": 11,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "ENST00000498257.6",
"gene_hgnc_id": 6482,
"gene_symbol": "LAMA2",
"hgvs_c": "c.76C>A",
"hgvs_p": "p.Pro26Thr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000510533.1",
"strand": true,
"transcript": "ENST00000498257.6",
"transcript_support_level": 5
},
{
"aa_alt": "T",
"aa_end": null,
"aa_length": 477,
"aa_ref": "P",
"aa_start": 26,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1750,
"cdna_start": 173,
"cds_end": null,
"cds_length": 1434,
"cds_start": 76,
"consequences": [
"missense_variant"
],
"exon_count": 10,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000688799.1",
"gene_hgnc_id": 6482,
"gene_symbol": "LAMA2",
"hgvs_c": "c.76C>A",
"hgvs_p": "p.Pro26Thr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000508458.1",
"strand": true,
"transcript": "ENST00000688799.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 3385,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 10,
"exon_rank": 10,
"exon_rank_end": null,
"feature": "ENST00000657779.1",
"gene_hgnc_id": null,
"gene_symbol": "ENSG00000226149",
"hgvs_c": "n.3273G>T",
"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": "ENST00000657779.1",
"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": 2528,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 10,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000688198.1",
"gene_hgnc_id": 6482,
"gene_symbol": "LAMA2",
"hgvs_c": "n.989C>A",
"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": "ENST00000688198.1",
"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": 4443,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 8,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "ENST00000690858.1",
"gene_hgnc_id": 6482,
"gene_symbol": "LAMA2",
"hgvs_c": "n.1005C>A",
"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": "ENST00000690858.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 1445,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 12,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000664071.1",
"gene_hgnc_id": null,
"gene_symbol": "ENSG00000226149",
"hgvs_c": "n.1372+8449G>T",
"hgvs_p": null,
"intron_rank": 11,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": false,
"transcript": "ENST00000664071.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 2743,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 10,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000665046.1",
"gene_hgnc_id": null,
"gene_symbol": "ENSG00000226149",
"hgvs_c": "n.975+10592G>T",
"hgvs_p": null,
"intron_rank": 9,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": false,
"transcript": "ENST00000665046.1",
"transcript_support_level": null
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs780695627",
"effect": "missense_variant",
"frequency_reference_population": 0.000049562488,
"gene_hgnc_id": 6482,
"gene_symbol": "LAMA2",
"gnomad_exomes_ac": 56,
"gnomad_exomes_af": 0.0000383095,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_ac": 24,
"gnomad_genomes_af": 0.000157538,
"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": "Conflicting classifications of pathogenicity",
"phenotype_combined": "not specified|Congenital muscular dystrophy due to partial LAMA2 deficiency|Muscular dystrophy, limb-girdle, autosomal recessive 23;Merosin deficient congenital muscular dystrophy|LAMA2-related muscular dystrophy|not provided",
"phylop100way_prediction": "Benign",
"phylop100way_score": 1.838,
"pos": 129492013,
"ref": "C",
"revel_prediction": "Benign",
"revel_score": 0.219,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0,
"transcript": "NM_000426.4"
}
]
}