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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: 2-169132617-A-G (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=2&pos=169132617&ref=A&alt=G&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "2",
"pos": 169132617,
"ref": "A",
"alt": "G",
"effect": "missense_variant",
"transcript": "NM_004525.3",
"consequences": [
{
"aa_ref": "V",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 77,
"exon_rank_end": null,
"exon_count": 79,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LRP2",
"gene_hgnc_id": 6694,
"hgvs_c": "c.13685T>C",
"hgvs_p": "p.Val4562Ala",
"transcript": "NM_004525.3",
"protein_id": "NP_004516.2",
"transcript_support_level": null,
"aa_start": 4562,
"aa_end": null,
"aa_length": 4655,
"cds_start": 13685,
"cds_end": null,
"cds_length": 13968,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000649046.1",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_004525.3"
},
{
"aa_ref": "V",
"aa_alt": "A",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 77,
"exon_rank_end": null,
"exon_count": 79,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LRP2",
"gene_hgnc_id": 6694,
"hgvs_c": "c.13685T>C",
"hgvs_p": "p.Val4562Ala",
"transcript": "ENST00000649046.1",
"protein_id": "ENSP00000496870.1",
"transcript_support_level": null,
"aa_start": 4562,
"aa_end": null,
"aa_length": 4655,
"cds_start": 13685,
"cds_end": null,
"cds_length": 13968,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_004525.3",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000649046.1"
},
{
"aa_ref": "V",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 76,
"exon_rank_end": null,
"exon_count": 78,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LRP2",
"gene_hgnc_id": 6694,
"hgvs_c": "c.13556T>C",
"hgvs_p": "p.Val4519Ala",
"transcript": "XM_011511183.4",
"protein_id": "XP_011509485.1",
"transcript_support_level": null,
"aa_start": 4519,
"aa_end": null,
"aa_length": 4612,
"cds_start": 13556,
"cds_end": null,
"cds_length": 13839,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_011511183.4"
},
{
"aa_ref": "V",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 77,
"exon_rank_end": null,
"exon_count": 79,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LRP2",
"gene_hgnc_id": 6694,
"hgvs_c": "c.12761T>C",
"hgvs_p": "p.Val4254Ala",
"transcript": "XM_047444340.1",
"protein_id": "XP_047300296.1",
"transcript_support_level": null,
"aa_start": 4254,
"aa_end": null,
"aa_length": 4347,
"cds_start": 12761,
"cds_end": null,
"cds_length": 13044,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047444340.1"
},
{
"aa_ref": "V",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 62,
"exon_rank_end": null,
"exon_count": 64,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LRP2",
"gene_hgnc_id": 6694,
"hgvs_c": "c.11396T>C",
"hgvs_p": "p.Val3799Ala",
"transcript": "XM_011511184.3",
"protein_id": "XP_011509486.1",
"transcript_support_level": null,
"aa_start": 3799,
"aa_end": null,
"aa_length": 3892,
"cds_start": 11396,
"cds_end": null,
"cds_length": 11679,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_011511184.3"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LRP2",
"gene_hgnc_id": 6694,
"hgvs_c": "n.539T>C",
"hgvs_p": null,
"transcript": "ENST00000491228.1",
"protein_id": null,
"transcript_support_level": 4,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "retained_intron",
"feature": "ENST00000491228.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 28,
"exon_rank_end": null,
"exon_count": 30,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LRP2",
"gene_hgnc_id": 6694,
"hgvs_c": "n.*409T>C",
"hgvs_p": null,
"transcript": "ENST00000649153.1",
"protein_id": "ENSP00000497617.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "nonsense_mediated_decay",
"feature": "ENST00000649153.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 22,
"exon_rank_end": null,
"exon_count": 24,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LRP2",
"gene_hgnc_id": 6694,
"hgvs_c": "n.*1359T>C",
"hgvs_p": null,
"transcript": "ENST00000650252.1",
"protein_id": "ENSP00000496887.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "nonsense_mediated_decay",
"feature": "ENST00000650252.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 28,
"exon_rank_end": null,
"exon_count": 30,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LRP2",
"gene_hgnc_id": 6694,
"hgvs_c": "n.*409T>C",
"hgvs_p": null,
"transcript": "ENST00000649153.1",
"protein_id": "ENSP00000497617.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "nonsense_mediated_decay",
"feature": "ENST00000649153.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 22,
"exon_rank_end": null,
"exon_count": 24,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LRP2",
"gene_hgnc_id": 6694,
"hgvs_c": "n.*1359T>C",
"hgvs_p": null,
"transcript": "ENST00000650252.1",
"protein_id": "ENSP00000496887.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "nonsense_mediated_decay",
"feature": "ENST00000650252.1"
}
],
"gene_symbol": "LRP2",
"gene_hgnc_id": 6694,
"dbsnp": "rs142245618",
"frequency_reference_population": 0.0028708105,
"hom_count_reference_population": 15,
"allele_count_reference_population": 4627,
"gnomad_exomes_af": 0.00297103,
"gnomad_genomes_af": 0.00191053,
"gnomad_exomes_ac": 4336,
"gnomad_genomes_ac": 291,
"gnomad_exomes_homalt": 15,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.004580110311508179,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.267,
"revel_prediction": "Benign",
"alphamissense_score": 0.0659,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.54,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": -0.58,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0,
"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": -13,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6,BS1,BS2",
"acmg_by_gene": [
{
"score": -13,
"benign_score": 13,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6",
"BS1",
"BS2"
],
"verdict": "Benign",
"transcript": "NM_004525.3",
"gene_symbol": "LRP2",
"hgnc_id": 6694,
"effects": [
"missense_variant"
],
"inheritance_mode": "AD,AR",
"hgvs_c": "c.13685T>C",
"hgvs_p": "p.Val4562Ala"
}
],
"clinvar_disease": "Donnai-Barrow syndrome,LRP2-related disorder,not provided,not specified",
"clinvar_classification": "Conflicting classifications of pathogenicity",
"clinvar_review_status": "criteria provided, conflicting classifications",
"clinvar_submissions_summary": "US:1 LB:4 B:1",
"phenotype_combined": "not specified|not provided|Donnai-Barrow syndrome|LRP2-related disorder",
"pathogenicity_classification_combined": "Conflicting classifications of pathogenicity",
"custom_annotations": null
}
],
"message": null
}