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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: 10-79559511-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=10&pos=79559511&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "10",
"pos": 79559511,
"ref": "C",
"alt": "T",
"effect": "splice_region_variant,intron_variant",
"transcript": "ENST00000372325.7",
"consequences": [
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "SFTPA2",
"gene_hgnc_id": 10799,
"hgvs_c": "c.-23-5G>A",
"hgvs_p": null,
"transcript": "NM_001098668.4",
"protein_id": "NP_001092138.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 248,
"cds_start": -4,
"cds_end": null,
"cds_length": 747,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2201,
"mane_select": "ENST00000372325.7",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "SFTPA2",
"gene_hgnc_id": 10799,
"hgvs_c": "c.-23-5G>A",
"hgvs_p": null,
"transcript": "ENST00000372325.7",
"protein_id": "ENSP00000361400.2",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 248,
"cds_start": -4,
"cds_end": null,
"cds_length": 747,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2201,
"mane_select": "NM_001098668.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "SFTPA2",
"gene_hgnc_id": 10799,
"hgvs_c": "c.-23-5G>A",
"hgvs_p": null,
"transcript": "ENST00000372327.9",
"protein_id": "ENSP00000361402.5",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 248,
"cds_start": -4,
"cds_end": null,
"cds_length": 747,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 815,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "SFTPA2",
"gene_hgnc_id": 10799,
"hgvs_c": "c.23-5G>A",
"hgvs_p": null,
"transcript": "ENST00000640627.1",
"protein_id": "ENSP00000492537.1",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 37,
"cds_start": -4,
"cds_end": null,
"cds_length": 114,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 195,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"5_prime_UTR_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SFTPA2",
"gene_hgnc_id": 10799,
"hgvs_c": "c.-28G>A",
"hgvs_p": null,
"transcript": "ENST00000492049.1",
"protein_id": "ENSP00000473275.1",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": 96,
"cds_start": -4,
"cds_end": null,
"cds_length": 293,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 644,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "SFTPA2",
"gene_hgnc_id": 10799,
"hgvs_c": "c.8-5G>A",
"hgvs_p": null,
"transcript": "NM_001320814.1",
"protein_id": "NP_001307743.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 258,
"cds_start": -4,
"cds_end": null,
"cds_length": 777,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2324,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_acceptor_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "SFTPA2",
"gene_hgnc_id": 10799,
"hgvs_c": "c.-26-2G>A",
"hgvs_p": null,
"transcript": "NM_001320813.2",
"protein_id": "NP_001307742.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 248,
"cds_start": -4,
"cds_end": null,
"cds_length": 747,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2204,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "SFTPA2",
"gene_hgnc_id": 10799,
"hgvs_c": "c.-23-5G>A",
"hgvs_p": null,
"transcript": "NM_001437428.1",
"protein_id": "NP_001424357.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 248,
"cds_start": -4,
"cds_end": null,
"cds_length": 747,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2138,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "SFTPA2",
"gene_hgnc_id": 10799,
"hgvs_c": "c.-23-5G>A",
"hgvs_p": null,
"transcript": "ENST00000417041.1",
"protein_id": "ENSP00000397375.1",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": 157,
"cds_start": -4,
"cds_end": null,
"cds_length": 474,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 726,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_acceptor_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "SFTPA2",
"gene_hgnc_id": 10799,
"hgvs_c": "c.29-2G>A",
"hgvs_p": null,
"transcript": "XM_017016608.2",
"protein_id": "XP_016872097.2",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 266,
"cds_start": -4,
"cds_end": null,
"cds_length": 801,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2244,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_acceptor_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "SFTPA2",
"gene_hgnc_id": 10799,
"hgvs_c": "c.29-2G>A",
"hgvs_p": null,
"transcript": "XM_047425703.1",
"protein_id": "XP_047281659.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 266,
"cds_start": -4,
"cds_end": null,
"cds_length": 801,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2337,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "SFTPA2",
"gene_hgnc_id": 10799,
"hgvs_c": "c.29-5G>A",
"hgvs_p": null,
"transcript": "XM_005270128.4",
"protein_id": "XP_005270185.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 265,
"cds_start": -4,
"cds_end": null,
"cds_length": 798,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2241,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "SFTPA2",
"gene_hgnc_id": 10799,
"hgvs_c": "c.29-5G>A",
"hgvs_p": null,
"transcript": "XM_047425704.1",
"protein_id": "XP_047281660.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 265,
"cds_start": -4,
"cds_end": null,
"cds_length": 798,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2334,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": 3,
"intron_rank_end": null,
"gene_symbol": "SFTPA2",
"gene_hgnc_id": 10799,
"hgvs_c": "c.23-5G>A",
"hgvs_p": null,
"transcript": "XM_047425705.1",
"protein_id": "XP_047281661.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 263,
"cds_start": -4,
"cds_end": null,
"cds_length": 792,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2301,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "SFTPA2",
"gene_hgnc_id": 10799,
"hgvs_c": "c.-23-5G>A",
"hgvs_p": null,
"transcript": "XM_011540125.2",
"protein_id": "XP_011538427.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 248,
"cds_start": -4,
"cds_end": null,
"cds_length": 747,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2294,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_acceptor_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "SFTPA2",
"gene_hgnc_id": 10799,
"hgvs_c": "c.-26-2G>A",
"hgvs_p": null,
"transcript": "XM_047425706.1",
"protein_id": "XP_047281662.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 248,
"cds_start": -4,
"cds_end": null,
"cds_length": 747,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2297,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "SFTPA2",
"gene_hgnc_id": 10799,
"dbsnp": "rs1650232",
"frequency_reference_population": 0.8017071,
"hom_count_reference_population": 480364,
"allele_count_reference_population": 1150044,
"gnomad_exomes_af": 0.810821,
"gnomad_genomes_af": 0.724201,
"gnomad_exomes_ac": 1040736,
"gnomad_genomes_ac": 109308,
"gnomad_exomes_homalt": 440365,
"gnomad_genomes_homalt": 39999,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": -0.9200000166893005,
"computational_prediction_selected": "Benign",
"computational_source_selected": "BayesDel_noAF",
"splice_score_selected": 0.5540000200271606,
"splice_prediction_selected": "Benign",
"splice_source_selected": "dbscSNV1_RF",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.92,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": -1.306,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0.63,
"spliceai_max_prediction": "Pathogenic",
"dbscsnv_ada_score": 0.708654309591697,
"dbscsnv_ada_prediction": "Benign",
"apogee2_score": null,
"apogee2_prediction": null,
"mitotip_score": null,
"mitotip_prediction": null,
"acmg_score": -20,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6_Very_Strong,BA1",
"acmg_by_gene": [
{
"score": -20,
"benign_score": 20,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong",
"BA1"
],
"verdict": "Benign",
"transcript": "ENST00000372325.7",
"gene_symbol": "SFTPA2",
"hgnc_id": 10799,
"effects": [
"splice_region_variant",
"intron_variant"
],
"inheritance_mode": "AD,Unknown",
"hgvs_c": "c.-23-5G>A",
"hgvs_p": null
}
],
"clinvar_disease": "Interstitial lung disease 2,SFTPA2-related disorder,not provided",
"clinvar_classification": "Benign",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "B:3",
"phenotype_combined": "not provided|Interstitial lung disease 2|SFTPA2-related disorder",
"pathogenicity_classification_combined": "Benign",
"custom_annotations": null
}
],
"message": null
}