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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: X-18246674-TCG-CAA (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=X&pos=18246674&ref=TCG&alt=CAA&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 0,
"criteria": [],
"effects": [
"missense_variant"
],
"gene_symbol": "SCML2",
"hgnc_id": 10581,
"hgvs_c": "c.1723_1725delCGAinsTTG",
"hgvs_p": "p.Arg575Leu",
"inheritance_mode": "",
"pathogenic_score": 0,
"score": 0,
"transcript": "NM_006089.3",
"verdict": "Uncertain_significance"
}
],
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "",
"acmg_score": 0,
"allele_count_reference_population": 0,
"alphamissense_prediction": null,
"alphamissense_score": null,
"alt": "CAA",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": null,
"bayesdelnoaf_score": null,
"chr": "X",
"clinvar_classification": "",
"clinvar_disease": "",
"clinvar_review_status": "",
"clinvar_submissions_summary": "",
"computational_prediction_selected": null,
"computational_score_selected": null,
"computational_source_selected": null,
"consequences": [
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 700,
"aa_ref": "R",
"aa_start": 575,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4162,
"cdna_start": 1846,
"cds_end": null,
"cds_length": 2103,
"cds_start": 1723,
"consequences": [
"missense_variant"
],
"exon_count": 15,
"exon_rank": null,
"exon_rank_end": null,
"feature": "NM_006089.3",
"gene_hgnc_id": 10581,
"gene_symbol": "SCML2",
"hgvs_c": "c.1723_1725delCGAinsTTG",
"hgvs_p": "p.Arg575Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000251900.9",
"protein_coding": true,
"protein_id": "NP_006080.1",
"strand": false,
"transcript": "NM_006089.3",
"transcript_support_level": null
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 700,
"aa_ref": "R",
"aa_start": 575,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 4162,
"cdna_start": 1846,
"cds_end": null,
"cds_length": 2103,
"cds_start": 1723,
"consequences": [
"missense_variant"
],
"exon_count": 15,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000251900.9",
"gene_hgnc_id": 10581,
"gene_symbol": "SCML2",
"hgvs_c": "c.1723_1725delCGAinsTTG",
"hgvs_p": "p.Arg575Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_006089.3",
"protein_coding": true,
"protein_id": "ENSP00000251900.4",
"strand": false,
"transcript": "ENST00000251900.9",
"transcript_support_level": 1
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 138,
"aa_ref": "R",
"aa_start": 13,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1334,
"cdna_start": 82,
"cds_end": null,
"cds_length": 417,
"cds_start": 37,
"consequences": [
"missense_variant"
],
"exon_count": 4,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000398048.4",
"gene_hgnc_id": 10581,
"gene_symbol": "SCML2",
"hgvs_c": "c.37_39delCGAinsTTG",
"hgvs_p": "p.Arg13Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000381126.4",
"strand": false,
"transcript": "ENST00000398048.4",
"transcript_support_level": 1
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 700,
"aa_ref": "R",
"aa_start": 575,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4153,
"cdna_start": 1838,
"cds_end": null,
"cds_length": 2103,
"cds_start": 1723,
"consequences": [
"missense_variant"
],
"exon_count": 15,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000926833.1",
"gene_hgnc_id": 10581,
"gene_symbol": "SCML2",
"hgvs_c": "c.1723_1725delCGAinsTTG",
"hgvs_p": "p.Arg575Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000596892.1",
"strand": false,
"transcript": "ENST00000926833.1",
"transcript_support_level": null
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 700,
"aa_ref": "R",
"aa_start": 575,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4281,
"cdna_start": 1966,
"cds_end": null,
"cds_length": 2103,
"cds_start": 1723,
"consequences": [
"missense_variant"
],
"exon_count": 16,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000926834.1",
"gene_hgnc_id": 10581,
"gene_symbol": "SCML2",
"hgvs_c": "c.1723_1725delCGAinsTTG",
"hgvs_p": "p.Arg575Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000596893.1",
"strand": false,
"transcript": "ENST00000926834.1",
"transcript_support_level": null
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 700,
"aa_ref": "R",
"aa_start": 575,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4269,
"cdna_start": 1947,
"cds_end": null,
"cds_length": 2103,
"cds_start": 1723,
"consequences": [
"missense_variant"
],
"exon_count": 15,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000926835.1",
"gene_hgnc_id": 10581,
"gene_symbol": "SCML2",
"hgvs_c": "c.1723_1725delCGAinsTTG",
"hgvs_p": "p.Arg575Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000596894.1",
"strand": false,
"transcript": "ENST00000926835.1",
"transcript_support_level": null
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 345,
"aa_ref": "R",
"aa_start": 311,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1514,
"cdna_start": 1160,
"cds_end": null,
"cds_length": 1038,
"cds_start": 931,
"consequences": [
"missense_variant"
],
"exon_count": 8,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000665583.1",
"gene_hgnc_id": 10581,
"gene_symbol": "SCML2",
"hgvs_c": "c.931_933delCGAinsTTG",
"hgvs_p": "p.Arg311Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000499630.1",
"strand": false,
"transcript": "ENST00000665583.1",
"transcript_support_level": null
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 123,
"aa_ref": "R",
"aa_start": 89,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2432,
"cdna_start": 269,
"cds_end": null,
"cds_length": 372,
"cds_start": 265,
"consequences": [
"missense_variant"
],
"exon_count": 3,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000420857.6",
"gene_hgnc_id": 10581,
"gene_symbol": "SCML2",
"hgvs_c": "c.265_267delCGAinsTTG",
"hgvs_p": "p.Arg89Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000407315.2",
"strand": false,
"transcript": "ENST00000420857.6",
"transcript_support_level": 2
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 700,
"aa_ref": "R",
"aa_start": 575,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4123,
"cdna_start": 1807,
"cds_end": null,
"cds_length": 2103,
"cds_start": 1723,
"consequences": [
"missense_variant"
],
"exon_count": 15,
"exon_rank": null,
"exon_rank_end": null,
"feature": "XM_017029219.2",
"gene_hgnc_id": 10581,
"gene_symbol": "SCML2",
"hgvs_c": "c.1723_1725delCGAinsTTG",
"hgvs_p": "p.Arg575Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_016884708.1",
"strand": false,
"transcript": "XM_017029219.2",
"transcript_support_level": null
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 700,
"aa_ref": "R",
"aa_start": 575,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4092,
"cdna_start": 1776,
"cds_end": null,
"cds_length": 2103,
"cds_start": 1723,
"consequences": [
"missense_variant"
],
"exon_count": 15,
"exon_rank": null,
"exon_rank_end": null,
"feature": "XM_017029220.3",
"gene_hgnc_id": 10581,
"gene_symbol": "SCML2",
"hgvs_c": "c.1723_1725delCGAinsTTG",
"hgvs_p": "p.Arg575Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_016884709.1",
"strand": false,
"transcript": "XM_017029220.3",
"transcript_support_level": null
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 609,
"aa_ref": "R",
"aa_start": 575,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4010,
"cdna_start": 1846,
"cds_end": null,
"cds_length": 1830,
"cds_start": 1723,
"consequences": [
"missense_variant"
],
"exon_count": 14,
"exon_rank": null,
"exon_rank_end": null,
"feature": "XM_006724458.1",
"gene_hgnc_id": 10581,
"gene_symbol": "SCML2",
"hgvs_c": "c.1723_1725delCGAinsTTG",
"hgvs_p": "p.Arg575Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_006724521.1",
"strand": false,
"transcript": "XM_006724458.1",
"transcript_support_level": null
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 436,
"aa_ref": "R",
"aa_start": 311,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 9233,
"cdna_start": 6917,
"cds_end": null,
"cds_length": 1311,
"cds_start": 931,
"consequences": [
"missense_variant"
],
"exon_count": 9,
"exon_rank": null,
"exon_rank_end": null,
"feature": "XM_017029222.2",
"gene_hgnc_id": 10581,
"gene_symbol": "SCML2",
"hgvs_c": "c.931_933delCGAinsTTG",
"hgvs_p": "p.Arg311Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_016884711.1",
"strand": false,
"transcript": "XM_017029222.2",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 3103,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 16,
"exon_rank": 13,
"exon_rank_end": null,
"feature": "NR_033717.2",
"gene_hgnc_id": 10581,
"gene_symbol": "SCML2",
"hgvs_c": "n.1844_1846delCGAinsTTG",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": false,
"transcript": "NR_033717.2",
"transcript_support_level": null
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": null,
"effect": "missense_variant",
"frequency_reference_population": null,
"gene_hgnc_id": 10581,
"gene_symbol": "SCML2",
"gnomad_exomes_ac": null,
"gnomad_exomes_af": null,
"gnomad_exomes_homalt": null,
"gnomad_genomes_ac": null,
"gnomad_genomes_af": null,
"gnomad_genomes_homalt": null,
"gnomad_mito_heteroplasmic": null,
"gnomad_mito_homoplasmic": null,
"hom_count_reference_population": 0,
"mitotip_prediction": null,
"mitotip_score": null,
"pathogenicity_classification_combined": null,
"phenotype_combined": null,
"phylop100way_prediction": "Benign",
"phylop100way_score": 1.974,
"pos": 18246674,
"ref": "TCG",
"revel_prediction": null,
"revel_score": null,
"splice_prediction_selected": null,
"splice_score_selected": null,
"splice_source_selected": null,
"spliceai_max_prediction": null,
"spliceai_max_score": null,
"transcript": "NM_006089.3"
}
]
}