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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: 5-78416647-A-G (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=5&pos=78416647&ref=A&alt=G&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "5",
"pos": 78416647,
"ref": "A",
"alt": "G",
"effect": "missense_variant,splice_region_variant",
"transcript": "NM_004866.6",
"consequences": [
{
"aa_ref": "H",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SCAMP1",
"gene_hgnc_id": 10563,
"hgvs_c": "c.341A>G",
"hgvs_p": "p.His114Arg",
"transcript": "NM_004866.6",
"protein_id": "NP_004857.4",
"transcript_support_level": null,
"aa_start": 114,
"aa_end": null,
"aa_length": 338,
"cds_start": 341,
"cds_end": null,
"cds_length": 1017,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000621999.5",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_004866.6"
},
{
"aa_ref": "H",
"aa_alt": "R",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SCAMP1",
"gene_hgnc_id": 10563,
"hgvs_c": "c.341A>G",
"hgvs_p": "p.His114Arg",
"transcript": "ENST00000621999.5",
"protein_id": "ENSP00000481022.1",
"transcript_support_level": 1,
"aa_start": 114,
"aa_end": null,
"aa_length": 338,
"cds_start": 341,
"cds_end": null,
"cds_length": 1017,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_004866.6",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000621999.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"splice_region_variant",
"non_coding_transcript_exon_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SCAMP1",
"gene_hgnc_id": 10563,
"hgvs_c": "n.341A>G",
"hgvs_p": null,
"transcript": "ENST00000614488.4",
"protein_id": "ENSP00000478071.1",
"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": null,
"mane_select": null,
"mane_plus": null,
"biotype": "nonsense_mediated_decay",
"feature": "ENST00000614488.4"
},
{
"aa_ref": "H",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SCAMP1",
"gene_hgnc_id": 10563,
"hgvs_c": "c.413A>G",
"hgvs_p": "p.His138Arg",
"transcript": "ENST00000878187.1",
"protein_id": "ENSP00000548246.1",
"transcript_support_level": null,
"aa_start": 138,
"aa_end": null,
"aa_length": 362,
"cds_start": 413,
"cds_end": null,
"cds_length": 1089,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000878187.1"
},
{
"aa_ref": "H",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SCAMP1",
"gene_hgnc_id": 10563,
"hgvs_c": "c.341A>G",
"hgvs_p": "p.His114Arg",
"transcript": "ENST00000962697.1",
"protein_id": "ENSP00000632756.1",
"transcript_support_level": null,
"aa_start": 114,
"aa_end": null,
"aa_length": 337,
"cds_start": 341,
"cds_end": null,
"cds_length": 1014,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000962697.1"
},
{
"aa_ref": "H",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SCAMP1",
"gene_hgnc_id": 10563,
"hgvs_c": "c.341A>G",
"hgvs_p": "p.His114Arg",
"transcript": "ENST00000878188.1",
"protein_id": "ENSP00000548247.1",
"transcript_support_level": null,
"aa_start": 114,
"aa_end": null,
"aa_length": 335,
"cds_start": 341,
"cds_end": null,
"cds_length": 1008,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000878188.1"
},
{
"aa_ref": "H",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SCAMP1",
"gene_hgnc_id": 10563,
"hgvs_c": "c.263A>G",
"hgvs_p": "p.His88Arg",
"transcript": "NM_001290229.2",
"protein_id": "NP_001277158.1",
"transcript_support_level": null,
"aa_start": 88,
"aa_end": null,
"aa_length": 312,
"cds_start": 263,
"cds_end": null,
"cds_length": 939,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001290229.2"
},
{
"aa_ref": "H",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SCAMP1",
"gene_hgnc_id": 10563,
"hgvs_c": "c.263A>G",
"hgvs_p": "p.His88Arg",
"transcript": "ENST00000618166.4",
"protein_id": "ENSP00000480865.1",
"transcript_support_level": 2,
"aa_start": 88,
"aa_end": null,
"aa_length": 312,
"cds_start": 263,
"cds_end": null,
"cds_length": 939,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000618166.4"
},
{
"aa_ref": "H",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SCAMP1",
"gene_hgnc_id": 10563,
"hgvs_c": "c.341A>G",
"hgvs_p": "p.His114Arg",
"transcript": "ENST00000920041.1",
"protein_id": "ENSP00000590100.1",
"transcript_support_level": null,
"aa_start": 114,
"aa_end": null,
"aa_length": 295,
"cds_start": 341,
"cds_end": null,
"cds_length": 888,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000920041.1"
},
{
"aa_ref": "H",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SCAMP1",
"gene_hgnc_id": 10563,
"hgvs_c": "c.44A>G",
"hgvs_p": "p.His15Arg",
"transcript": "ENST00000320280.8",
"protein_id": "ENSP00000478292.1",
"transcript_support_level": 3,
"aa_start": 15,
"aa_end": null,
"aa_length": 205,
"cds_start": 44,
"cds_end": null,
"cds_length": 618,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000320280.8"
},
{
"aa_ref": "H",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SCAMP1",
"gene_hgnc_id": 10563,
"hgvs_c": "c.341A>G",
"hgvs_p": "p.His114Arg",
"transcript": "XM_011543727.4",
"protein_id": "XP_011542029.1",
"transcript_support_level": null,
"aa_start": 114,
"aa_end": null,
"aa_length": 304,
"cds_start": 341,
"cds_end": null,
"cds_length": 915,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_011543727.4"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"splice_region_variant",
"non_coding_transcript_exon_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SCAMP1",
"gene_hgnc_id": 10563,
"hgvs_c": "n.396A>G",
"hgvs_p": null,
"transcript": "NR_110885.2",
"protein_id": null,
"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": "pseudogene",
"feature": "NR_110885.2"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"downstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SCAMP1",
"gene_hgnc_id": 10563,
"hgvs_c": "c.*12A>G",
"hgvs_p": null,
"transcript": "ENST00000511551.2",
"protein_id": "ENSP00000482491.1",
"transcript_support_level": 4,
"aa_start": null,
"aa_end": null,
"aa_length": 118,
"cds_start": null,
"cds_end": null,
"cds_length": 359,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000511551.2"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"downstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SCAMP1",
"gene_hgnc_id": 10563,
"hgvs_c": "c.*59A>G",
"hgvs_p": null,
"transcript": "ENST00000510030.2",
"protein_id": "ENSP00000478205.1",
"transcript_support_level": 4,
"aa_start": null,
"aa_end": null,
"aa_length": 41,
"cds_start": null,
"cds_end": null,
"cds_length": 126,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000510030.2"
}
],
"gene_symbol": "SCAMP1",
"gene_hgnc_id": 10563,
"dbsnp": "rs1354791577",
"frequency_reference_population": 0.0000021064604,
"hom_count_reference_population": 0,
"allele_count_reference_population": 3,
"gnomad_exomes_af": 0.00000210646,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": 3,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.15393629670143127,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.27000001072883606,
"splice_prediction_selected": "Uncertain_significance",
"splice_source_selected": "max_spliceai",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": 0.1077,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.22,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 3.597,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0.27,
"spliceai_max_prediction": "Uncertain_significance",
"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_004866.6",
"gene_symbol": "SCAMP1",
"hgnc_id": 10563,
"effects": [
"missense_variant",
"splice_region_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.341A>G",
"hgvs_p": "p.His114Arg"
}
],
"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
}