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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: 22-50698779-A-ATGAGGC (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=22&pos=50698779&ref=A&alt=ATGAGGC&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "22",
"pos": 50698779,
"ref": "A",
"alt": "ATGAGGC",
"effect": "disruptive_inframe_insertion",
"transcript": "ENST00000692848.2",
"consequences": [
{
"aa_ref": "Q",
"aa_alt": "LRQ",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"disruptive_inframe_insertion"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 25,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SHANK3",
"gene_hgnc_id": 14294,
"hgvs_c": "c.1775_1780dupTGAGGC",
"hgvs_p": "p.Arg593_Gln594insLeuArg",
"transcript": "NM_001372044.2",
"protein_id": "NP_001358973.1",
"transcript_support_level": null,
"aa_start": 594,
"aa_end": null,
"aa_length": 1793,
"cds_start": 1781,
"cds_end": null,
"cds_length": 5382,
"cdna_start": 2151,
"cdna_end": null,
"cdna_length": 7652,
"mane_select": "ENST00000710353.1",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Q",
"aa_alt": "LRQ",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"disruptive_inframe_insertion"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SHANK3",
"gene_hgnc_id": 14294,
"hgvs_c": "c.1772_1777dupTGAGGC",
"hgvs_p": "p.Arg592_Gln593insLeuArg",
"transcript": "ENST00000692848.2",
"protein_id": "ENSP00000510794.2",
"transcript_support_level": null,
"aa_start": 593,
"aa_end": null,
"aa_length": 1792,
"cds_start": 1778,
"cds_end": null,
"cds_length": 5379,
"cdna_start": 1785,
"cdna_end": null,
"cdna_length": 7286,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Q",
"aa_alt": "LRQ",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"disruptive_inframe_insertion"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SHANK3",
"gene_hgnc_id": 14294,
"hgvs_c": "c.1190_1195dupTGAGGC",
"hgvs_p": "p.Arg398_Gln399insLeuArg",
"transcript": "ENST00000262795.8",
"protein_id": "ENSP00000489147.3",
"transcript_support_level": 5,
"aa_start": 399,
"aa_end": null,
"aa_length": 1598,
"cds_start": 1196,
"cds_end": null,
"cds_length": 4797,
"cdna_start": 1646,
"cdna_end": null,
"cdna_length": 7147,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SHANK3",
"gene_hgnc_id": 14294,
"hgvs_c": "n.1774_1779dupTGAGGC",
"hgvs_p": null,
"transcript": "ENST00000414786.8",
"protein_id": null,
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 7281,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SHANK3",
"gene_hgnc_id": 14294,
"hgvs_c": "n.215_220dupTGAGGC",
"hgvs_p": null,
"transcript": "ENST00000673838.1",
"protein_id": null,
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 297,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SHANK3",
"gene_hgnc_id": 14294,
"hgvs_c": "n.1772_1777dupTGAGGC",
"hgvs_p": null,
"transcript": "ENST00000673971.3",
"protein_id": "ENSP00000501192.2",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 7982,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SHANK3",
"gene_hgnc_id": 14294,
"hgvs_c": "n.*177_*182dupTGAGGC",
"hgvs_p": null,
"transcript": "ENST00000673995.1",
"protein_id": "ENSP00000500960.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 525,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SHANK3",
"gene_hgnc_id": 14294,
"hgvs_c": "n.435_440dupTGAGGC",
"hgvs_p": null,
"transcript": "ENST00000674010.1",
"protein_id": null,
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 517,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SHANK3",
"gene_hgnc_id": 14294,
"hgvs_c": "n.782_787dupTGAGGC",
"hgvs_p": null,
"transcript": "ENST00000674145.1",
"protein_id": null,
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 864,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SHANK3",
"gene_hgnc_id": 14294,
"hgvs_c": "n.*177_*182dupTGAGGC",
"hgvs_p": null,
"transcript": "ENST00000673995.1",
"protein_id": "ENSP00000500960.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 525,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "SHANK3",
"gene_hgnc_id": 14294,
"dbsnp": "rs1555908096",
"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": 3.208,
"phylop100way_prediction": "Benign",
"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": 4,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2,PM4",
"acmg_by_gene": [
{
"score": 4,
"benign_score": 0,
"pathogenic_score": 4,
"criteria": [
"PM2",
"PM4"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000692848.2",
"gene_symbol": "SHANK3",
"hgnc_id": 14294,
"effects": [
"disruptive_inframe_insertion"
],
"inheritance_mode": "AD",
"hgvs_c": "c.1772_1777dupTGAGGC",
"hgvs_p": "p.Arg592_Gln593insLeuArg"
}
],
"clinvar_disease": "Inborn genetic diseases",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"phenotype_combined": "Inborn genetic diseases",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}