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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: 13-48261205-A-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=13&pos=48261205&ref=A&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "13",
"pos": 48261205,
"ref": "A",
"alt": "C",
"effect": "missense_variant",
"transcript": "NM_021999.5",
"consequences": [
{
"aa_ref": "E",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ITM2B",
"gene_hgnc_id": 6174,
"hgvs_c": "c.782A>C",
"hgvs_p": "p.Glu261Ala",
"transcript": "NM_021999.5",
"protein_id": "NP_068839.1",
"transcript_support_level": null,
"aa_start": 261,
"aa_end": null,
"aa_length": 266,
"cds_start": 782,
"cds_end": null,
"cds_length": 801,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000647800.2",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_021999.5"
},
{
"aa_ref": "E",
"aa_alt": "A",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ITM2B",
"gene_hgnc_id": 6174,
"hgvs_c": "c.782A>C",
"hgvs_p": "p.Glu261Ala",
"transcript": "ENST00000647800.2",
"protein_id": "ENSP00000497221.1",
"transcript_support_level": null,
"aa_start": 261,
"aa_end": null,
"aa_length": 266,
"cds_start": 782,
"cds_end": null,
"cds_length": 801,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_021999.5",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000647800.2"
},
{
"aa_ref": "E",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ITM2B",
"gene_hgnc_id": 6174,
"hgvs_c": "c.848A>C",
"hgvs_p": "p.Glu283Ala",
"transcript": "ENST00000970638.1",
"protein_id": "ENSP00000640697.1",
"transcript_support_level": null,
"aa_start": 283,
"aa_end": null,
"aa_length": 288,
"cds_start": 848,
"cds_end": null,
"cds_length": 867,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000970638.1"
},
{
"aa_ref": "E",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ITM2B",
"gene_hgnc_id": 6174,
"hgvs_c": "c.746A>C",
"hgvs_p": "p.Glu249Ala",
"transcript": "ENST00000899433.1",
"protein_id": "ENSP00000569492.1",
"transcript_support_level": null,
"aa_start": 249,
"aa_end": null,
"aa_length": 254,
"cds_start": 746,
"cds_end": null,
"cds_length": 765,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000899433.1"
},
{
"aa_ref": "E",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ITM2B",
"gene_hgnc_id": 6174,
"hgvs_c": "c.722A>C",
"hgvs_p": "p.Glu241Ala",
"transcript": "ENST00000899432.1",
"protein_id": "ENSP00000569491.1",
"transcript_support_level": null,
"aa_start": 241,
"aa_end": null,
"aa_length": 246,
"cds_start": 722,
"cds_end": null,
"cds_length": 741,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000899432.1"
},
{
"aa_ref": "E",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ITM2B",
"gene_hgnc_id": 6174,
"hgvs_c": "c.671A>C",
"hgvs_p": "p.Glu224Ala",
"transcript": "ENST00000899431.1",
"protein_id": "ENSP00000569490.1",
"transcript_support_level": null,
"aa_start": 224,
"aa_end": null,
"aa_length": 229,
"cds_start": 671,
"cds_end": null,
"cds_length": 690,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000899431.1"
},
{
"aa_ref": "E",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ITM2B",
"gene_hgnc_id": 6174,
"hgvs_c": "c.653A>C",
"hgvs_p": "p.Glu218Ala",
"transcript": "ENST00000970637.1",
"protein_id": "ENSP00000640696.1",
"transcript_support_level": null,
"aa_start": 218,
"aa_end": null,
"aa_length": 223,
"cds_start": 653,
"cds_end": null,
"cds_length": 672,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000970637.1"
},
{
"aa_ref": "E",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ITM2B",
"gene_hgnc_id": 6174,
"hgvs_c": "c.614A>C",
"hgvs_p": "p.Glu205Ala",
"transcript": "ENST00000649266.1",
"protein_id": "ENSP00000498127.1",
"transcript_support_level": null,
"aa_start": 205,
"aa_end": null,
"aa_length": 210,
"cds_start": 614,
"cds_end": null,
"cds_length": 633,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000649266.1"
},
{
"aa_ref": "E",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ITM2B",
"gene_hgnc_id": 6174,
"hgvs_c": "c.464A>C",
"hgvs_p": "p.Glu155Ala",
"transcript": "ENST00000378549.5",
"protein_id": "ENSP00000367811.5",
"transcript_support_level": 5,
"aa_start": 155,
"aa_end": null,
"aa_length": 160,
"cds_start": 464,
"cds_end": null,
"cds_length": 483,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000378549.5"
},
{
"aa_ref": "K",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ITM2B",
"gene_hgnc_id": 6174,
"hgvs_c": "c.193A>C",
"hgvs_p": "p.Lys65Gln",
"transcript": "ENST00000650237.1",
"protein_id": "ENSP00000497296.1",
"transcript_support_level": null,
"aa_start": 65,
"aa_end": null,
"aa_length": 66,
"cds_start": 193,
"cds_end": null,
"cds_length": 201,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000650237.1"
},
{
"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": "ITM2B",
"gene_hgnc_id": 6174,
"hgvs_c": "n.65A>C",
"hgvs_p": null,
"transcript": "ENST00000463839.3",
"protein_id": "ENSP00000476004.2",
"transcript_support_level": 3,
"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": "ENST00000463839.3"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ITM2B",
"gene_hgnc_id": 6174,
"hgvs_c": "n.830A>C",
"hgvs_p": null,
"transcript": "ENST00000648312.1",
"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": "ENST00000648312.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ITM2B",
"gene_hgnc_id": 6174,
"hgvs_c": "n.860A>C",
"hgvs_p": null,
"transcript": "ENST00000648586.1",
"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": "ENST00000648586.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ITM2B",
"gene_hgnc_id": 6174,
"hgvs_c": "n.712A>C",
"hgvs_p": null,
"transcript": "ENST00000648898.1",
"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": "ENST00000648898.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ITM2B",
"gene_hgnc_id": 6174,
"hgvs_c": "n.*528A>C",
"hgvs_p": null,
"transcript": "ENST00000649452.1",
"protein_id": "ENSP00000497877.1",
"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": "nonsense_mediated_decay",
"feature": "ENST00000649452.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ITM2B",
"gene_hgnc_id": 6174,
"hgvs_c": "n.*528A>C",
"hgvs_p": null,
"transcript": "ENST00000649452.1",
"protein_id": "ENSP00000497877.1",
"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": "nonsense_mediated_decay",
"feature": "ENST00000649452.1"
}
],
"gene_symbol": "ITM2B",
"gene_hgnc_id": 6174,
"dbsnp": "rs606231283",
"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": 0.859684407711029,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.885,
"revel_prediction": "Pathogenic",
"alphamissense_score": 0.6749,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.21,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 8.571,
"phylop100way_prediction": "Pathogenic",
"spliceai_max_score": 0,
"spliceai_max_prediction": "Benign",
"dbscsnv_ada_score": null,
"dbscsnv_ada_prediction": null,
"apogee2_score": null,
"apogee2_prediction": null,
"mitotip_score": null,
"mitotip_prediction": null,
"acmg_score": 5,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2,PP3_Moderate,PP5",
"acmg_by_gene": [
{
"score": 5,
"benign_score": 0,
"pathogenic_score": 5,
"criteria": [
"PM2",
"PP3_Moderate",
"PP5"
],
"verdict": "Uncertain_significance",
"transcript": "NM_021999.5",
"gene_symbol": "ITM2B",
"hgnc_id": 6174,
"effects": [
"missense_variant"
],
"inheritance_mode": "AD",
"hgvs_c": "c.782A>C",
"hgvs_p": "p.Glu261Ala"
}
],
"clinvar_disease": "Retinal dystrophy with inner retinal dysfunction and ganglion cell anomalies",
"clinvar_classification": "Pathogenic",
"clinvar_review_status": "no assertion criteria provided",
"clinvar_submissions_summary": "null",
"phenotype_combined": "Retinal dystrophy with inner retinal dysfunction and ganglion cell anomalies",
"pathogenicity_classification_combined": "Pathogenic",
"custom_annotations": null
}
],
"message": null
}