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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: 19-41838213-G-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=19&pos=41838213&ref=G&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "19",
"pos": 41838213,
"ref": "G",
"alt": "C",
"effect": "missense_variant",
"transcript": "NM_173506.7",
"consequences": [
{
"aa_ref": "S",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LYPD4",
"gene_hgnc_id": 28659,
"hgvs_c": "c.260C>G",
"hgvs_p": "p.Ser87Cys",
"transcript": "NM_173506.7",
"protein_id": "NP_775777.3",
"transcript_support_level": null,
"aa_start": 87,
"aa_end": null,
"aa_length": 246,
"cds_start": 260,
"cds_end": null,
"cds_length": 741,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000609812.6",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_173506.7"
},
{
"aa_ref": "S",
"aa_alt": "C",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LYPD4",
"gene_hgnc_id": 28659,
"hgvs_c": "c.260C>G",
"hgvs_p": "p.Ser87Cys",
"transcript": "ENST00000609812.6",
"protein_id": "ENSP00000476510.1",
"transcript_support_level": 1,
"aa_start": 87,
"aa_end": null,
"aa_length": 246,
"cds_start": 260,
"cds_end": null,
"cds_length": 741,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_173506.7",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000609812.6"
},
{
"aa_ref": "S",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LYPD4",
"gene_hgnc_id": 28659,
"hgvs_c": "c.155C>G",
"hgvs_p": "p.Ser52Cys",
"transcript": "ENST00000343055.5",
"protein_id": "ENSP00000339568.4",
"transcript_support_level": 1,
"aa_start": 52,
"aa_end": null,
"aa_length": 211,
"cds_start": 155,
"cds_end": null,
"cds_length": 636,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000343055.5"
},
{
"aa_ref": "S",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LYPD4",
"gene_hgnc_id": 28659,
"hgvs_c": "c.155C>G",
"hgvs_p": "p.Ser52Cys",
"transcript": "NM_001291419.2",
"protein_id": "NP_001278348.1",
"transcript_support_level": null,
"aa_start": 52,
"aa_end": null,
"aa_length": 211,
"cds_start": 155,
"cds_end": null,
"cds_length": 636,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001291419.2"
},
{
"aa_ref": "S",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LYPD4",
"gene_hgnc_id": 28659,
"hgvs_c": "c.155C>G",
"hgvs_p": "p.Ser52Cys",
"transcript": "ENST00000601246.5",
"protein_id": "ENSP00000472570.1",
"transcript_support_level": 5,
"aa_start": 52,
"aa_end": null,
"aa_length": 211,
"cds_start": 155,
"cds_end": null,
"cds_length": 636,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000601246.5"
},
{
"aa_ref": "S",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LYPD4",
"gene_hgnc_id": 28659,
"hgvs_c": "c.299C>G",
"hgvs_p": "p.Ser100Cys",
"transcript": "XM_005258543.3",
"protein_id": "XP_005258600.1",
"transcript_support_level": null,
"aa_start": 100,
"aa_end": null,
"aa_length": 259,
"cds_start": 299,
"cds_end": null,
"cds_length": 780,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_005258543.3"
},
{
"aa_ref": "S",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LYPD4",
"gene_hgnc_id": 28659,
"hgvs_c": "c.299C>G",
"hgvs_p": "p.Ser100Cys",
"transcript": "XM_005278383.6",
"protein_id": "XP_005278440.1",
"transcript_support_level": null,
"aa_start": 100,
"aa_end": null,
"aa_length": 259,
"cds_start": 299,
"cds_end": null,
"cds_length": 780,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_005278383.6"
},
{
"aa_ref": "S",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LYPD4",
"gene_hgnc_id": 28659,
"hgvs_c": "c.299C>G",
"hgvs_p": "p.Ser100Cys",
"transcript": "XM_011526483.2",
"protein_id": "XP_011524785.1",
"transcript_support_level": null,
"aa_start": 100,
"aa_end": null,
"aa_length": 259,
"cds_start": 299,
"cds_end": null,
"cds_length": 780,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_011526483.2"
},
{
"aa_ref": "S",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LYPD4",
"gene_hgnc_id": 28659,
"hgvs_c": "c.299C>G",
"hgvs_p": "p.Ser100Cys",
"transcript": "XM_011526484.3",
"protein_id": "XP_011524786.1",
"transcript_support_level": null,
"aa_start": 100,
"aa_end": null,
"aa_length": 259,
"cds_start": 299,
"cds_end": null,
"cds_length": 780,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_011526484.3"
},
{
"aa_ref": "S",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LYPD4",
"gene_hgnc_id": 28659,
"hgvs_c": "c.287C>G",
"hgvs_p": "p.Ser96Cys",
"transcript": "XM_006723035.3",
"protein_id": "XP_006723098.1",
"transcript_support_level": null,
"aa_start": 96,
"aa_end": null,
"aa_length": 255,
"cds_start": 287,
"cds_end": null,
"cds_length": 768,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_006723035.3"
},
{
"aa_ref": "S",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LYPD4",
"gene_hgnc_id": 28659,
"hgvs_c": "c.299C>G",
"hgvs_p": "p.Ser100Cys",
"transcript": "XM_005278385.6",
"protein_id": "XP_005278442.1",
"transcript_support_level": null,
"aa_start": 100,
"aa_end": null,
"aa_length": 254,
"cds_start": 299,
"cds_end": null,
"cds_length": 765,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_005278385.6"
},
{
"aa_ref": "S",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LYPD4",
"gene_hgnc_id": 28659,
"hgvs_c": "c.260C>G",
"hgvs_p": "p.Ser87Cys",
"transcript": "XM_024451373.2",
"protein_id": "XP_024307141.1",
"transcript_support_level": null,
"aa_start": 87,
"aa_end": null,
"aa_length": 246,
"cds_start": 260,
"cds_end": null,
"cds_length": 741,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_024451373.2"
},
{
"aa_ref": "S",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LYPD4",
"gene_hgnc_id": 28659,
"hgvs_c": "c.260C>G",
"hgvs_p": "p.Ser87Cys",
"transcript": "XM_024451375.2",
"protein_id": "XP_024307143.1",
"transcript_support_level": null,
"aa_start": 87,
"aa_end": null,
"aa_length": 241,
"cds_start": 260,
"cds_end": null,
"cds_length": 726,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_024451375.2"
},
{
"aa_ref": "S",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LYPD4",
"gene_hgnc_id": 28659,
"hgvs_c": "c.299C>G",
"hgvs_p": "p.Ser100Cys",
"transcript": "XM_005278387.6",
"protein_id": "XP_005278444.1",
"transcript_support_level": null,
"aa_start": 100,
"aa_end": null,
"aa_length": 210,
"cds_start": 299,
"cds_end": null,
"cds_length": 633,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_005278387.6"
},
{
"aa_ref": "S",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LYPD4",
"gene_hgnc_id": 28659,
"hgvs_c": "c.113C>G",
"hgvs_p": "p.Ser38Cys",
"transcript": "XM_005278388.5",
"protein_id": "XP_005278445.1",
"transcript_support_level": null,
"aa_start": 38,
"aa_end": null,
"aa_length": 197,
"cds_start": 113,
"cds_end": null,
"cds_length": 594,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_005278388.5"
},
{
"aa_ref": "S",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LYPD4",
"gene_hgnc_id": 28659,
"hgvs_c": "c.260C>G",
"hgvs_p": "p.Ser87Cys",
"transcript": "XM_024451376.2",
"protein_id": "XP_024307144.1",
"transcript_support_level": null,
"aa_start": 87,
"aa_end": null,
"aa_length": 197,
"cds_start": 260,
"cds_end": null,
"cds_length": 594,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_024451376.2"
},
{
"aa_ref": "S",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LYPD4",
"gene_hgnc_id": 28659,
"hgvs_c": "c.260C>G",
"hgvs_p": "p.Ser87Cys",
"transcript": "XM_024451378.2",
"protein_id": "XP_024307146.1",
"transcript_support_level": null,
"aa_start": 87,
"aa_end": null,
"aa_length": 197,
"cds_start": 260,
"cds_end": null,
"cds_length": 594,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_024451378.2"
}
],
"gene_symbol": "LYPD4",
"gene_hgnc_id": 28659,
"dbsnp": "rs781990787",
"frequency_reference_population": 0.0000131473425,
"hom_count_reference_population": 0,
"allele_count_reference_population": 2,
"gnomad_exomes_af": null,
"gnomad_genomes_af": 0.0000131473,
"gnomad_exomes_ac": null,
"gnomad_genomes_ac": 2,
"gnomad_exomes_homalt": null,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.4506181478500366,
"computational_prediction_selected": "Uncertain_significance",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.124,
"revel_prediction": "Benign",
"alphamissense_score": 0.5622,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.47,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 3.751,
"phylop100way_prediction": "Uncertain_significance",
"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": 2,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2",
"acmg_by_gene": [
{
"score": 2,
"benign_score": 0,
"pathogenic_score": 2,
"criteria": [
"PM2"
],
"verdict": "Uncertain_significance",
"transcript": "NM_173506.7",
"gene_symbol": "LYPD4",
"hgnc_id": 28659,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.260C>G",
"hgvs_p": "p.Ser87Cys"
}
],
"clinvar_disease": "not specified",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"phenotype_combined": "not specified",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}