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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: 6-5260579-C-G (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=6&pos=5260579&ref=C&alt=G&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 14,
"criteria": [
"BP4_Strong",
"BP6_Moderate",
"BA1"
],
"effects": [
"intron_variant"
],
"gene_symbol": "LYRM4",
"hgnc_id": 21365,
"hgvs_c": "c.86+69G>C",
"hgvs_p": null,
"inheritance_mode": "Unknown,AR",
"pathogenic_score": 0,
"score": -14,
"transcript": "NM_001164840.3",
"verdict": "Benign"
},
{
"benign_score": 14,
"criteria": [
"BP4_Strong",
"BP6_Moderate",
"BA1"
],
"effects": [
"intron_variant"
],
"gene_symbol": "FARS2",
"hgnc_id": 21062,
"hgvs_c": "c.-22+10626C>G",
"hgvs_p": null,
"inheritance_mode": "AR",
"pathogenic_score": 0,
"score": -14,
"transcript": "XM_047418086.1",
"verdict": "Benign"
}
],
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6_Moderate,BA1",
"acmg_score": -14,
"allele_count_reference_population": 274940,
"alphamissense_prediction": null,
"alphamissense_score": null,
"alt": "G",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Benign",
"bayesdelnoaf_score": -0.9,
"chr": "6",
"clinvar_classification": "Benign",
"clinvar_disease": "not provided",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "B:1",
"computational_prediction_selected": "Benign",
"computational_score_selected": -0.8999999761581421,
"computational_source_selected": "BayesDel_noAF",
"consequences": [
{
"aa_alt": null,
"aa_end": null,
"aa_length": 91,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1497,
"cdna_start": null,
"cds_end": null,
"cds_length": 276,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 3,
"exon_rank": null,
"exon_rank_end": null,
"feature": "NM_020408.6",
"gene_hgnc_id": 21365,
"gene_symbol": "LYRM4",
"hgvs_c": "c.86+69G>C",
"hgvs_p": null,
"intron_rank": 1,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000330636.9",
"protein_coding": true,
"protein_id": "NP_065141.3",
"strand": false,
"transcript": "NM_020408.6",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 91,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 1497,
"cdna_start": null,
"cds_end": null,
"cds_length": 276,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 3,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000330636.9",
"gene_hgnc_id": 21365,
"gene_symbol": "LYRM4",
"hgvs_c": "c.86+69G>C",
"hgvs_p": null,
"intron_rank": 1,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_020408.6",
"protein_coding": true,
"protein_id": "ENSP00000418787.1",
"strand": false,
"transcript": "ENST00000330636.9",
"transcript_support_level": 1
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 70,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 941,
"cdna_start": null,
"cds_end": null,
"cds_length": 213,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 4,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000480566.5",
"gene_hgnc_id": 21365,
"gene_symbol": "LYRM4",
"hgvs_c": "c.86+69G>C",
"hgvs_p": null,
"intron_rank": 1,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000419928.1",
"strand": false,
"transcript": "ENST00000480566.5",
"transcript_support_level": 1
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 40,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1168,
"cdna_start": null,
"cds_end": null,
"cds_length": 123,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 2,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000468929.5",
"gene_hgnc_id": 21365,
"gene_symbol": "LYRM4",
"hgvs_c": "c.86+69G>C",
"hgvs_p": null,
"intron_rank": 1,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000418321.1",
"strand": false,
"transcript": "ENST00000468929.5",
"transcript_support_level": 1
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 130,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 805,
"cdna_start": null,
"cds_end": null,
"cds_length": 393,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 3,
"exon_rank": null,
"exon_rank_end": null,
"feature": "NM_001164840.3",
"gene_hgnc_id": 21365,
"gene_symbol": "LYRM4",
"hgvs_c": "c.86+69G>C",
"hgvs_p": null,
"intron_rank": 1,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001158312.1",
"strand": false,
"transcript": "NM_001164840.3",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 130,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 592,
"cdna_start": null,
"cds_end": null,
"cds_length": 393,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 3,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000500576.4",
"gene_hgnc_id": 21365,
"gene_symbol": "LYRM4",
"hgvs_c": "c.86+69G>C",
"hgvs_p": null,
"intron_rank": 1,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000443900.3",
"strand": false,
"transcript": "ENST00000500576.4",
"transcript_support_level": 2
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 115,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 764,
"cdna_start": null,
"cds_end": null,
"cds_length": 348,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 3,
"exon_rank": null,
"exon_rank_end": null,
"feature": "NM_001318783.1",
"gene_hgnc_id": 21365,
"gene_symbol": "LYRM4",
"hgvs_c": "c.86+69G>C",
"hgvs_p": null,
"intron_rank": 1,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001305712.1",
"strand": false,
"transcript": "NM_001318783.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 96,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1622,
"cdna_start": null,
"cds_end": null,
"cds_length": 291,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 4,
"exon_rank": null,
"exon_rank_end": null,
"feature": "NM_001164841.3",
"gene_hgnc_id": 21365,
"gene_symbol": "LYRM4",
"hgvs_c": "c.86+69G>C",
"hgvs_p": null,
"intron_rank": 1,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001158313.1",
"strand": false,
"transcript": "NM_001164841.3",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 96,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1401,
"cdna_start": null,
"cds_end": null,
"cds_length": 291,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 4,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000464010.5",
"gene_hgnc_id": 21365,
"gene_symbol": "LYRM4",
"hgvs_c": "c.86+69G>C",
"hgvs_p": null,
"intron_rank": 1,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000420026.1",
"strand": false,
"transcript": "ENST00000464010.5",
"transcript_support_level": 3
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 86,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1449,
"cdna_start": null,
"cds_end": null,
"cds_length": 261,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 3,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000912483.1",
"gene_hgnc_id": 21365,
"gene_symbol": "LYRM4",
"hgvs_c": "c.86+69G>C",
"hgvs_p": null,
"intron_rank": 1,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000582542.1",
"strand": false,
"transcript": "ENST00000912483.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 70,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1149,
"cdna_start": null,
"cds_end": null,
"cds_length": 213,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 4,
"exon_rank": null,
"exon_rank_end": null,
"feature": "NM_001318782.1",
"gene_hgnc_id": 21365,
"gene_symbol": "LYRM4",
"hgvs_c": "c.86+69G>C",
"hgvs_p": null,
"intron_rank": 1,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001305711.1",
"strand": false,
"transcript": "NM_001318782.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 451,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1551,
"cdna_start": null,
"cds_end": null,
"cds_length": 1356,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 7,
"exon_rank": null,
"exon_rank_end": null,
"feature": "XM_047418086.1",
"gene_hgnc_id": 21062,
"gene_symbol": "FARS2",
"hgvs_c": "c.-22+10626C>G",
"hgvs_p": null,
"intron_rank": 1,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_047274042.1",
"strand": true,
"transcript": "XM_047418086.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 129,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3435,
"cdna_start": null,
"cds_end": null,
"cds_length": 390,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 4,
"exon_rank": null,
"exon_rank_end": null,
"feature": "XM_017011084.3",
"gene_hgnc_id": 21365,
"gene_symbol": "LYRM4",
"hgvs_c": "c.86+69G>C",
"hgvs_p": null,
"intron_rank": 1,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_016866573.1",
"strand": false,
"transcript": "XM_017011084.3",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 97,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 876,
"cdna_start": null,
"cds_end": null,
"cds_length": 294,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 4,
"exon_rank": null,
"exon_rank_end": null,
"feature": "XM_017011083.3",
"gene_hgnc_id": 21365,
"gene_symbol": "LYRM4",
"hgvs_c": "c.86+69G>C",
"hgvs_p": null,
"intron_rank": 1,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_016866572.1",
"strand": false,
"transcript": "XM_017011083.3",
"transcript_support_level": null
},
{
"aa_alt": null,
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"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 450,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 3,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000455814.2",
"gene_hgnc_id": 21365,
"gene_symbol": "LYRM4",
"hgvs_c": "n.74+69G>C",
"hgvs_p": null,
"intron_rank": 1,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": false,
"transcript": "ENST00000455814.2",
"transcript_support_level": 3
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 1844,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 4,
"exon_rank": null,
"exon_rank_end": null,
"feature": "NR_104417.2",
"gene_hgnc_id": 21365,
"gene_symbol": "LYRM4",
"hgvs_c": "n.303+69G>C",
"hgvs_p": null,
"intron_rank": 1,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": false,
"transcript": "NR_104417.2",
"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": 1376,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 2,
"exon_rank": null,
"exon_rank_end": null,
"feature": "NR_104418.1",
"gene_hgnc_id": 21365,
"gene_symbol": "LYRM4",
"hgvs_c": "n.303+69G>C",
"hgvs_p": null,
"intron_rank": 1,
"intron_rank_end": null,
"mane_plus": null,
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"protein_coding": false,
"protein_id": null,
"strand": false,
"transcript": "NR_104418.1",
"transcript_support_level": null
},
{
"aa_alt": null,
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"aa_length": null,
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"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 856,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 4,
"exon_rank": null,
"exon_rank_end": null,
"feature": "NR_134856.1",
"gene_hgnc_id": 21365,
"gene_symbol": "LYRM4",
"hgvs_c": "n.303+69G>C",
"hgvs_p": null,
"intron_rank": 1,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": false,
"transcript": "NR_134856.1",
"transcript_support_level": null
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs7752203",
"effect": "intron_variant",
"frequency_reference_population": 0.21716397,
"gene_hgnc_id": 21365,
"gene_symbol": "LYRM4",
"gnomad_exomes_ac": 215146,
"gnomad_exomes_af": 0.193122,
"gnomad_exomes_homalt": 36522,
"gnomad_genomes_ac": 59794,
"gnomad_genomes_af": 0.393371,
"gnomad_genomes_homalt": 15378,
"gnomad_mito_heteroplasmic": null,
"gnomad_mito_homoplasmic": null,
"hom_count_reference_population": 51900,
"mitotip_prediction": null,
"mitotip_score": null,
"pathogenicity_classification_combined": "Benign",
"phenotype_combined": "not provided",
"phylop100way_prediction": "Benign",
"phylop100way_score": -1.025,
"pos": 5260579,
"ref": "C",
"revel_prediction": null,
"revel_score": null,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0,
"transcript": "NM_001164840.3"
}
]
}