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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: 1-183222115-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=1&pos=183222115&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 0,
"criteria": [
"PVS1",
"PS3",
"PM2",
"PP5_Very_Strong"
],
"effects": [
"stop_gained"
],
"gene_symbol": "LAMC2",
"hgnc_id": 6493,
"hgvs_c": "c.667C>T",
"hgvs_p": "p.Arg223*",
"inheritance_mode": "AR",
"pathogenic_score": 22,
"score": 22,
"transcript": "NM_005562.3",
"verdict": "Pathogenic"
}
],
"acmg_classification": "Pathogenic",
"acmg_criteria": "PVS1,PS3,PM2,PP5_Very_Strong",
"acmg_score": 22,
"allele_count_reference_population": 3,
"alphamissense_prediction": null,
"alphamissense_score": null,
"alt": "T",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Pathogenic",
"bayesdelnoaf_score": 0.57,
"chr": "1",
"clinvar_classification": "Pathogenic",
"clinvar_disease": " intermediate, junctional 3A, junctional 3B, severe,Epidermolysis bullosa,Junctional epidermolysis bullosa gravis of Herlitz,not provided",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "P:3",
"computational_prediction_selected": "Pathogenic",
"computational_score_selected": 0.5699999928474426,
"computational_source_selected": "BayesDel_noAF",
"consequences": [
{
"aa_alt": "*",
"aa_end": null,
"aa_length": 1193,
"aa_ref": "R",
"aa_start": 223,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5398,
"cdna_start": 756,
"cds_end": null,
"cds_length": 3582,
"cds_start": 667,
"consequences": [
"stop_gained"
],
"exon_count": 23,
"exon_rank": 6,
"exon_rank_end": null,
"feature": "NM_005562.3",
"gene_hgnc_id": 6493,
"gene_symbol": "LAMC2",
"hgvs_c": "c.667C>T",
"hgvs_p": "p.Arg223*",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000264144.5",
"protein_coding": true,
"protein_id": "NP_005553.2",
"strand": true,
"transcript": "NM_005562.3",
"transcript_support_level": null
},
{
"aa_alt": "*",
"aa_end": null,
"aa_length": 1193,
"aa_ref": "R",
"aa_start": 223,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 5398,
"cdna_start": 756,
"cds_end": null,
"cds_length": 3582,
"cds_start": 667,
"consequences": [
"stop_gained"
],
"exon_count": 23,
"exon_rank": 6,
"exon_rank_end": null,
"feature": "ENST00000264144.5",
"gene_hgnc_id": 6493,
"gene_symbol": "LAMC2",
"hgvs_c": "c.667C>T",
"hgvs_p": "p.Arg223*",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_005562.3",
"protein_coding": true,
"protein_id": "ENSP00000264144.4",
"strand": true,
"transcript": "ENST00000264144.5",
"transcript_support_level": 1
},
{
"aa_alt": "*",
"aa_end": null,
"aa_length": 1111,
"aa_ref": "R",
"aa_start": 223,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4313,
"cdna_start": 782,
"cds_end": null,
"cds_length": 3336,
"cds_start": 667,
"consequences": [
"stop_gained"
],
"exon_count": 22,
"exon_rank": 6,
"exon_rank_end": null,
"feature": "ENST00000493293.5",
"gene_hgnc_id": 6493,
"gene_symbol": "LAMC2",
"hgvs_c": "c.667C>T",
"hgvs_p": "p.Arg223*",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000432063.1",
"strand": true,
"transcript": "ENST00000493293.5",
"transcript_support_level": 1
},
{
"aa_alt": "*",
"aa_end": null,
"aa_length": 1201,
"aa_ref": "R",
"aa_start": 223,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4808,
"cdna_start": 707,
"cds_end": null,
"cds_length": 3606,
"cds_start": 667,
"consequences": [
"stop_gained"
],
"exon_count": 23,
"exon_rank": 6,
"exon_rank_end": null,
"feature": "ENST00000914499.1",
"gene_hgnc_id": 6493,
"gene_symbol": "LAMC2",
"hgvs_c": "c.667C>T",
"hgvs_p": "p.Arg223*",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000584558.1",
"strand": true,
"transcript": "ENST00000914499.1",
"transcript_support_level": null
},
{
"aa_alt": "*",
"aa_end": null,
"aa_length": 1151,
"aa_ref": "R",
"aa_start": 181,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4720,
"cdna_start": 643,
"cds_end": null,
"cds_length": 3456,
"cds_start": 541,
"consequences": [
"stop_gained"
],
"exon_count": 23,
"exon_rank": 6,
"exon_rank_end": null,
"feature": "ENST00000878928.1",
"gene_hgnc_id": 6493,
"gene_symbol": "LAMC2",
"hgvs_c": "c.541C>T",
"hgvs_p": "p.Arg181*",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000548987.1",
"strand": true,
"transcript": "ENST00000878928.1",
"transcript_support_level": null
},
{
"aa_alt": "*",
"aa_end": null,
"aa_length": 1130,
"aa_ref": "R",
"aa_start": 160,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5007,
"cdna_start": 596,
"cds_end": null,
"cds_length": 3393,
"cds_start": 478,
"consequences": [
"stop_gained"
],
"exon_count": 22,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "ENST00000878925.1",
"gene_hgnc_id": 6493,
"gene_symbol": "LAMC2",
"hgvs_c": "c.478C>T",
"hgvs_p": "p.Arg160*",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000548984.1",
"strand": true,
"transcript": "ENST00000878925.1",
"transcript_support_level": null
},
{
"aa_alt": "*",
"aa_end": null,
"aa_length": 1120,
"aa_ref": "R",
"aa_start": 223,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4816,
"cdna_start": 963,
"cds_end": null,
"cds_length": 3363,
"cds_start": 667,
"consequences": [
"stop_gained"
],
"exon_count": 22,
"exon_rank": 6,
"exon_rank_end": null,
"feature": "ENST00000971656.1",
"gene_hgnc_id": 6493,
"gene_symbol": "LAMC2",
"hgvs_c": "c.667C>T",
"hgvs_p": "p.Arg223*",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000641715.1",
"strand": true,
"transcript": "ENST00000971656.1",
"transcript_support_level": null
},
{
"aa_alt": "*",
"aa_end": null,
"aa_length": 1111,
"aa_ref": "R",
"aa_start": 223,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4320,
"cdna_start": 756,
"cds_end": null,
"cds_length": 3336,
"cds_start": 667,
"consequences": [
"stop_gained"
],
"exon_count": 22,
"exon_rank": 6,
"exon_rank_end": null,
"feature": "NM_018891.3",
"gene_hgnc_id": 6493,
"gene_symbol": "LAMC2",
"hgvs_c": "c.667C>T",
"hgvs_p": "p.Arg223*",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_061486.2",
"strand": true,
"transcript": "NM_018891.3",
"transcript_support_level": null
},
{
"aa_alt": "*",
"aa_end": null,
"aa_length": 1111,
"aa_ref": "R",
"aa_start": 223,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4610,
"cdna_start": 779,
"cds_end": null,
"cds_length": 3336,
"cds_start": 667,
"consequences": [
"stop_gained"
],
"exon_count": 22,
"exon_rank": 6,
"exon_rank_end": null,
"feature": "ENST00000878926.1",
"gene_hgnc_id": 6493,
"gene_symbol": "LAMC2",
"hgvs_c": "c.667C>T",
"hgvs_p": "p.Arg223*",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000548985.1",
"strand": true,
"transcript": "ENST00000878926.1",
"transcript_support_level": null
},
{
"aa_alt": "*",
"aa_end": null,
"aa_length": 1097,
"aa_ref": "R",
"aa_start": 127,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4646,
"cdna_start": 569,
"cds_end": null,
"cds_length": 3294,
"cds_start": 379,
"consequences": [
"stop_gained"
],
"exon_count": 21,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "ENST00000914498.1",
"gene_hgnc_id": 6493,
"gene_symbol": "LAMC2",
"hgvs_c": "c.379C>T",
"hgvs_p": "p.Arg127*",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000584557.1",
"strand": true,
"transcript": "ENST00000914498.1",
"transcript_support_level": null
},
{
"aa_alt": "*",
"aa_end": null,
"aa_length": 1048,
"aa_ref": "R",
"aa_start": 160,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4783,
"cdna_start": 615,
"cds_end": null,
"cds_length": 3147,
"cds_start": 478,
"consequences": [
"stop_gained"
],
"exon_count": 21,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "ENST00000971655.1",
"gene_hgnc_id": 6493,
"gene_symbol": "LAMC2",
"hgvs_c": "c.478C>T",
"hgvs_p": "p.Arg160*",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000641714.1",
"strand": true,
"transcript": "ENST00000971655.1",
"transcript_support_level": null
},
{
"aa_alt": "*",
"aa_end": null,
"aa_length": 1191,
"aa_ref": "R",
"aa_start": 223,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3691,
"cdna_start": 756,
"cds_end": null,
"cds_length": 3576,
"cds_start": 667,
"consequences": [
"stop_gained"
],
"exon_count": 24,
"exon_rank": 6,
"exon_rank_end": null,
"feature": "XM_047420358.1",
"gene_hgnc_id": 6493,
"gene_symbol": "LAMC2",
"hgvs_c": "c.667C>T",
"hgvs_p": "p.Arg223*",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_047276314.1",
"strand": true,
"transcript": "XM_047420358.1",
"transcript_support_level": null
},
{
"aa_alt": "*",
"aa_end": null,
"aa_length": 1182,
"aa_ref": "R",
"aa_start": 223,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3664,
"cdna_start": 756,
"cds_end": null,
"cds_length": 3549,
"cds_start": 667,
"consequences": [
"stop_gained"
],
"exon_count": 23,
"exon_rank": 6,
"exon_rank_end": null,
"feature": "XM_047420361.1",
"gene_hgnc_id": 6493,
"gene_symbol": "LAMC2",
"hgvs_c": "c.667C>T",
"hgvs_p": "p.Arg223*",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_047276317.1",
"strand": true,
"transcript": "XM_047420361.1",
"transcript_support_level": null
},
{
"aa_alt": "*",
"aa_end": null,
"aa_length": 742,
"aa_ref": "R",
"aa_start": 223,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2403,
"cdna_start": 756,
"cds_end": null,
"cds_length": 2229,
"cds_start": 667,
"consequences": [
"stop_gained"
],
"exon_count": 15,
"exon_rank": 6,
"exon_rank_end": null,
"feature": "XM_017001273.2",
"gene_hgnc_id": 6493,
"gene_symbol": "LAMC2",
"hgvs_c": "c.667C>T",
"hgvs_p": "p.Arg223*",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_016856762.1",
"strand": true,
"transcript": "XM_017001273.2",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 1152,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4733,
"cdna_start": null,
"cds_end": null,
"cds_length": 3459,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 22,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000878927.1",
"gene_hgnc_id": 6493,
"gene_symbol": "LAMC2",
"hgvs_c": "c.641-1020C>T",
"hgvs_p": null,
"intron_rank": 5,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000548986.1",
"strand": true,
"transcript": "ENST00000878927.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 1010,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4282,
"cdna_start": null,
"cds_end": null,
"cds_length": 3033,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 19,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000971657.1",
"gene_hgnc_id": 6493,
"gene_symbol": "LAMC2",
"hgvs_c": "c.405-3493C>T",
"hgvs_p": null,
"intron_rank": 3,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000641716.1",
"strand": true,
"transcript": "ENST00000971657.1",
"transcript_support_level": null
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs753268823",
"effect": "stop_gained",
"frequency_reference_population": 0.0000020521998,
"gene_hgnc_id": 6493,
"gene_symbol": "LAMC2",
"gnomad_exomes_ac": 3,
"gnomad_exomes_af": 0.0000020522,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_ac": null,
"gnomad_genomes_af": null,
"gnomad_genomes_homalt": null,
"gnomad_mito_heteroplasmic": null,
"gnomad_mito_homoplasmic": null,
"hom_count_reference_population": 0,
"mitotip_prediction": null,
"mitotip_score": null,
"pathogenicity_classification_combined": "Pathogenic",
"phenotype_combined": "Junctional epidermolysis bullosa gravis of Herlitz|not provided|Epidermolysis bullosa, junctional 3A, intermediate;Epidermolysis bullosa, junctional 3B, severe",
"phylop100way_prediction": "Benign",
"phylop100way_score": 0.65,
"pos": 183222115,
"ref": "C",
"revel_prediction": null,
"revel_score": null,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0.10000000149011612,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0.1,
"transcript": "NM_005562.3"
}
]
}