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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: 16-2300001-GCACCTT-TGG (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=16&pos=2300001&ref=GCACCTT&alt=TGG&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "16",
"pos": 2300001,
"ref": "GCACCTT",
"alt": "TGG",
"effect": "splice_donor_variant,conservative_inframe_deletion,splice_region_variant,synonymous_variant,intron_variant",
"transcript": "NM_001089.3",
"consequences": [
{
"aa_ref": "K",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_donor_variant",
"conservative_inframe_deletion",
"splice_region_variant",
"synonymous_variant",
"intron_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 33,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ABCA3",
"gene_hgnc_id": 33,
"hgvs_c": "c.1609_1611+4delAAGGTGCinsCCA",
"hgvs_p": "p.Lys537del",
"transcript": "NM_001089.3",
"protein_id": "NP_001080.2",
"transcript_support_level": null,
"aa_start": 537,
"aa_end": null,
"aa_length": 1704,
"cds_start": 1609,
"cds_end": null,
"cds_length": 5115,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 6602,
"mane_select": "ENST00000301732.10",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001089.3"
},
{
"aa_ref": "K",
"aa_alt": null,
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_donor_variant",
"conservative_inframe_deletion",
"splice_region_variant",
"synonymous_variant",
"intron_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 33,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ABCA3",
"gene_hgnc_id": 33,
"hgvs_c": "c.1609_1611+4delAAGGTGCinsCCA",
"hgvs_p": "p.Lys537del",
"transcript": "ENST00000301732.10",
"protein_id": "ENSP00000301732.5",
"transcript_support_level": 1,
"aa_start": 537,
"aa_end": null,
"aa_length": 1704,
"cds_start": 1609,
"cds_end": null,
"cds_length": 5115,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 6602,
"mane_select": "NM_001089.3",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000301732.10"
},
{
"aa_ref": "K",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_donor_variant",
"conservative_inframe_deletion",
"splice_region_variant",
"synonymous_variant",
"intron_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 32,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ABCA3",
"gene_hgnc_id": 33,
"hgvs_c": "c.1435_1437+4delAAGGTGCinsCCA",
"hgvs_p": "p.Lys479del",
"transcript": "ENST00000382381.7",
"protein_id": "ENSP00000371818.3",
"transcript_support_level": 1,
"aa_start": 479,
"aa_end": null,
"aa_length": 1646,
"cds_start": 1435,
"cds_end": null,
"cds_length": 4941,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 6446,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000382381.7"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"splice_donor_variant",
"splice_region_variant",
"intron_variant",
"non_coding_transcript_exon_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ABCA3",
"gene_hgnc_id": 33,
"hgvs_c": "n.2172_2174+4delAAGGTGCinsCCA",
"hgvs_p": null,
"transcript": "ENST00000563623.5",
"protein_id": null,
"transcript_support_level": 1,
"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": 3649,
"mane_select": null,
"mane_plus": null,
"biotype": "retained_intron",
"feature": "ENST00000563623.5"
},
{
"aa_ref": "K",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_donor_variant",
"conservative_inframe_deletion",
"splice_region_variant",
"synonymous_variant",
"intron_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 33,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ABCA3",
"gene_hgnc_id": 33,
"hgvs_c": "c.1609_1611+4delAAGGTGCinsCCA",
"hgvs_p": "p.Lys537del",
"transcript": "ENST00000967440.1",
"protein_id": "ENSP00000637499.1",
"transcript_support_level": null,
"aa_start": 537,
"aa_end": null,
"aa_length": 1704,
"cds_start": 1609,
"cds_end": null,
"cds_length": 5115,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 6591,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000967440.1"
},
{
"aa_ref": "K",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_donor_variant",
"conservative_inframe_deletion",
"splice_region_variant",
"synonymous_variant",
"intron_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 33,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ABCA3",
"gene_hgnc_id": 33,
"hgvs_c": "c.1609_1611+4delAAGGTGCinsCCA",
"hgvs_p": "p.Lys537del",
"transcript": "ENST00000967441.1",
"protein_id": "ENSP00000637500.1",
"transcript_support_level": null,
"aa_start": 537,
"aa_end": null,
"aa_length": 1704,
"cds_start": 1609,
"cds_end": null,
"cds_length": 5115,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 6862,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000967441.1"
},
{
"aa_ref": "K",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_donor_variant",
"conservative_inframe_deletion",
"splice_region_variant",
"synonymous_variant",
"intron_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 32,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ABCA3",
"gene_hgnc_id": 33,
"hgvs_c": "c.1609_1611+4delAAGGTGCinsCCA",
"hgvs_p": "p.Lys537del",
"transcript": "ENST00000967443.1",
"protein_id": "ENSP00000637502.1",
"transcript_support_level": null,
"aa_start": 537,
"aa_end": null,
"aa_length": 1704,
"cds_start": 1609,
"cds_end": null,
"cds_length": 5115,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 6268,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000967443.1"
},
{
"aa_ref": "K",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_donor_variant",
"conservative_inframe_deletion",
"splice_region_variant",
"synonymous_variant",
"intron_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 33,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ABCA3",
"gene_hgnc_id": 33,
"hgvs_c": "c.1609_1611+4delAAGGTGCinsCCA",
"hgvs_p": "p.Lys537del",
"transcript": "ENST00000937273.1",
"protein_id": "ENSP00000607332.1",
"transcript_support_level": null,
"aa_start": 537,
"aa_end": null,
"aa_length": 1679,
"cds_start": 1609,
"cds_end": null,
"cds_length": 5040,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 6539,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000937273.1"
},
{
"aa_ref": "K",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_donor_variant",
"conservative_inframe_deletion",
"splice_region_variant",
"synonymous_variant",
"intron_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 33,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ABCA3",
"gene_hgnc_id": 33,
"hgvs_c": "c.1435_1437+4delAAGGTGCinsCCA",
"hgvs_p": "p.Lys479del",
"transcript": "ENST00000967439.1",
"protein_id": "ENSP00000637498.1",
"transcript_support_level": null,
"aa_start": 479,
"aa_end": null,
"aa_length": 1675,
"cds_start": 1435,
"cds_end": null,
"cds_length": 5028,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 6458,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000967439.1"
},
{
"aa_ref": "K",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_donor_variant",
"conservative_inframe_deletion",
"splice_region_variant",
"synonymous_variant",
"intron_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 32,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ABCA3",
"gene_hgnc_id": 33,
"hgvs_c": "c.1492_1494+4delAAGGTGCinsCCA",
"hgvs_p": "p.Lys498del",
"transcript": "ENST00000967438.1",
"protein_id": "ENSP00000637497.1",
"transcript_support_level": null,
"aa_start": 498,
"aa_end": null,
"aa_length": 1665,
"cds_start": 1492,
"cds_end": null,
"cds_length": 4998,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 6477,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000967438.1"
},
{
"aa_ref": "K",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_donor_variant",
"conservative_inframe_deletion",
"splice_region_variant",
"synonymous_variant",
"intron_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 33,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ABCA3",
"gene_hgnc_id": 33,
"hgvs_c": "c.1609_1611+4delAAGGTGCinsCCA",
"hgvs_p": "p.Lys537del",
"transcript": "ENST00000883065.1",
"protein_id": "ENSP00000553124.1",
"transcript_support_level": null,
"aa_start": 537,
"aa_end": null,
"aa_length": 1655,
"cds_start": 1609,
"cds_end": null,
"cds_length": 4968,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 6477,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000883065.1"
},
{
"aa_ref": "K",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_donor_variant",
"conservative_inframe_deletion",
"splice_region_variant",
"synonymous_variant",
"intron_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 32,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ABCA3",
"gene_hgnc_id": 33,
"hgvs_c": "c.1609_1611+4delAAGGTGCinsCCA",
"hgvs_p": "p.Lys537del",
"transcript": "ENST00000967442.1",
"protein_id": "ENSP00000637501.1",
"transcript_support_level": null,
"aa_start": 537,
"aa_end": null,
"aa_length": 1655,
"cds_start": 1609,
"cds_end": null,
"cds_length": 4968,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 6736,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000967442.1"
},
{
"aa_ref": "K",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_donor_variant",
"conservative_inframe_deletion",
"splice_region_variant",
"synonymous_variant",
"intron_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 32,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ABCA3",
"gene_hgnc_id": 33,
"hgvs_c": "c.1435_1437+4delAAGGTGCinsCCA",
"hgvs_p": "p.Lys479del",
"transcript": "ENST00000937274.1",
"protein_id": "ENSP00000607333.1",
"transcript_support_level": null,
"aa_start": 479,
"aa_end": null,
"aa_length": 1646,
"cds_start": 1435,
"cds_end": null,
"cds_length": 4941,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 6368,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000937274.1"
}
],
"gene_symbol": "ABCA3",
"gene_hgnc_id": 33,
"dbsnp": "rs876657633",
"frequency_reference_population": null,
"hom_count_reference_population": 0,
"allele_count_reference_population": 0,
"gnomad_exomes_af": null,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": null,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": null,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": null,
"computational_prediction_selected": null,
"computational_source_selected": null,
"splice_score_selected": null,
"splice_prediction_selected": null,
"splice_source_selected": null,
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": null,
"bayesdelnoaf_prediction": null,
"phylop100way_score": 8.23,
"phylop100way_prediction": "Pathogenic",
"spliceai_max_score": null,
"spliceai_max_prediction": null,
"dbscsnv_ada_score": null,
"dbscsnv_ada_prediction": null,
"apogee2_score": null,
"apogee2_prediction": null,
"mitotip_score": null,
"mitotip_prediction": null,
"acmg_score": 6,
"acmg_classification": "Likely_pathogenic",
"acmg_criteria": "PVS1_Moderate,PM2,PP5_Moderate",
"acmg_by_gene": [
{
"score": 6,
"benign_score": 0,
"pathogenic_score": 6,
"criteria": [
"PVS1_Moderate",
"PM2",
"PP5_Moderate"
],
"verdict": "Likely_pathogenic",
"transcript": "NM_001089.3",
"gene_symbol": "ABCA3",
"hgnc_id": 33,
"effects": [
"splice_donor_variant",
"conservative_inframe_deletion",
"splice_region_variant",
"synonymous_variant",
"intron_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.1609_1611+4delAAGGTGCinsCCA",
"hgvs_p": "p.Lys537del"
}
],
"clinvar_disease": "Diffuse interstitial pulmonary fibrosis,Primary interstitial lung disease specific to childhood due to pulmonary surfactant protein anomalies",
"clinvar_classification": "Likely pathogenic",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "LP:1",
"phenotype_combined": "Primary interstitial lung disease specific to childhood due to pulmonary surfactant protein anomalies;Diffuse interstitial pulmonary fibrosis",
"pathogenicity_classification_combined": "Likely pathogenic",
"custom_annotations": null
}
],
"message": null
}