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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: 7-12231904-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=7&pos=12231904&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 0,
"criteria": [
"PM2",
"PM5",
"PP3_Strong",
"PP5_Very_Strong"
],
"effects": [
"missense_variant"
],
"gene_symbol": "TMEM106B",
"hgnc_id": 22407,
"hgvs_c": "c.754G>A",
"hgvs_p": "p.Asp252Asn",
"inheritance_mode": "AD",
"pathogenic_score": 16,
"score": 16,
"transcript": "NM_018374.4",
"verdict": "Pathogenic"
}
],
"acmg_classification": "Pathogenic",
"acmg_criteria": "PM2,PM5,PP3_Strong,PP5_Very_Strong",
"acmg_score": 16,
"allele_count_reference_population": 0,
"alphamissense_prediction": null,
"alphamissense_score": 0.968,
"alt": "A",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Benign",
"bayesdelnoaf_score": -0.29,
"chr": "7",
"clinvar_classification": "Pathogenic/Likely pathogenic",
"clinvar_disease": " 16, hypomyelinating,Leukodystrophy,not provided",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "P:5 LP:2",
"computational_prediction_selected": "Pathogenic",
"computational_score_selected": 0.9645248651504517,
"computational_source_selected": "MetaRNN",
"consequences": [
{
"aa_alt": "N",
"aa_end": null,
"aa_length": 274,
"aa_ref": "D",
"aa_start": 252,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 12351,
"cdna_start": 888,
"cds_end": null,
"cds_length": 825,
"cds_start": 754,
"consequences": [
"missense_variant"
],
"exon_count": 8,
"exon_rank": 8,
"exon_rank_end": null,
"feature": "NM_001134232.2",
"gene_hgnc_id": 22407,
"gene_symbol": "TMEM106B",
"hgvs_c": "c.754G>A",
"hgvs_p": "p.Asp252Asn",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000396668.8",
"protein_coding": true,
"protein_id": "NP_001127704.1",
"strand": true,
"transcript": "NM_001134232.2",
"transcript_support_level": null
},
{
"aa_alt": "N",
"aa_end": null,
"aa_length": 274,
"aa_ref": "D",
"aa_start": 252,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 12351,
"cdna_start": 888,
"cds_end": null,
"cds_length": 825,
"cds_start": 754,
"consequences": [
"missense_variant"
],
"exon_count": 8,
"exon_rank": 8,
"exon_rank_end": null,
"feature": "ENST00000396668.8",
"gene_hgnc_id": 22407,
"gene_symbol": "TMEM106B",
"hgvs_c": "c.754G>A",
"hgvs_p": "p.Asp252Asn",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_001134232.2",
"protein_coding": true,
"protein_id": "ENSP00000379902.3",
"strand": true,
"transcript": "ENST00000396668.8",
"transcript_support_level": 1
},
{
"aa_alt": "N",
"aa_end": null,
"aa_length": 274,
"aa_ref": "D",
"aa_start": 252,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 12539,
"cdna_start": 1076,
"cds_end": null,
"cds_length": 825,
"cds_start": 754,
"consequences": [
"missense_variant"
],
"exon_count": 9,
"exon_rank": 9,
"exon_rank_end": null,
"feature": "ENST00000396667.7",
"gene_hgnc_id": 22407,
"gene_symbol": "TMEM106B",
"hgvs_c": "c.754G>A",
"hgvs_p": "p.Asp252Asn",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000379901.2",
"strand": true,
"transcript": "ENST00000396667.7",
"transcript_support_level": 1
},
{
"aa_alt": "N",
"aa_end": null,
"aa_length": 274,
"aa_ref": "D",
"aa_start": 252,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 12545,
"cdna_start": 1082,
"cds_end": null,
"cds_length": 825,
"cds_start": 754,
"consequences": [
"missense_variant"
],
"exon_count": 9,
"exon_rank": 9,
"exon_rank_end": null,
"feature": "NM_018374.4",
"gene_hgnc_id": 22407,
"gene_symbol": "TMEM106B",
"hgvs_c": "c.754G>A",
"hgvs_p": "p.Asp252Asn",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_060844.2",
"strand": true,
"transcript": "NM_018374.4",
"transcript_support_level": null
},
{
"aa_alt": "N",
"aa_end": null,
"aa_length": 274,
"aa_ref": "D",
"aa_start": 252,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 6300,
"cdna_start": 1008,
"cds_end": null,
"cds_length": 825,
"cds_start": 754,
"consequences": [
"missense_variant"
],
"exon_count": 8,
"exon_rank": 8,
"exon_rank_end": null,
"feature": "ENST00000444443.6",
"gene_hgnc_id": 22407,
"gene_symbol": "TMEM106B",
"hgvs_c": "c.754G>A",
"hgvs_p": "p.Asp252Asn",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000401302.2",
"strand": true,
"transcript": "ENST00000444443.6",
"transcript_support_level": 4
},
{
"aa_alt": "N",
"aa_end": null,
"aa_length": 274,
"aa_ref": "D",
"aa_start": 252,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1102,
"cdna_start": 969,
"cds_end": null,
"cds_length": 825,
"cds_start": 754,
"consequences": [
"missense_variant"
],
"exon_count": 8,
"exon_rank": 8,
"exon_rank_end": null,
"feature": "ENST00000704455.1",
"gene_hgnc_id": 22407,
"gene_symbol": "TMEM106B",
"hgvs_c": "c.754G>A",
"hgvs_p": "p.Asp252Asn",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000515905.1",
"strand": true,
"transcript": "ENST00000704455.1",
"transcript_support_level": null
},
{
"aa_alt": "N",
"aa_end": null,
"aa_length": 274,
"aa_ref": "D",
"aa_start": 252,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2773,
"cdna_start": 987,
"cds_end": null,
"cds_length": 825,
"cds_start": 754,
"consequences": [
"missense_variant"
],
"exon_count": 9,
"exon_rank": 9,
"exon_rank_end": null,
"feature": "ENST00000903751.1",
"gene_hgnc_id": 22407,
"gene_symbol": "TMEM106B",
"hgvs_c": "c.754G>A",
"hgvs_p": "p.Asp252Asn",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000573810.1",
"strand": true,
"transcript": "ENST00000903751.1",
"transcript_support_level": null
},
{
"aa_alt": "N",
"aa_end": null,
"aa_length": 274,
"aa_ref": "D",
"aa_start": 252,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2342,
"cdna_start": 1157,
"cds_end": null,
"cds_length": 825,
"cds_start": 754,
"consequences": [
"missense_variant"
],
"exon_count": 8,
"exon_rank": 8,
"exon_rank_end": null,
"feature": "ENST00000965695.1",
"gene_hgnc_id": 22407,
"gene_symbol": "TMEM106B",
"hgvs_c": "c.754G>A",
"hgvs_p": "p.Asp252Asn",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000635754.1",
"strand": true,
"transcript": "ENST00000965695.1",
"transcript_support_level": null
},
{
"aa_alt": "N",
"aa_end": null,
"aa_length": 274,
"aa_ref": "D",
"aa_start": 252,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1632,
"cdna_start": 816,
"cds_end": null,
"cds_length": 825,
"cds_start": 754,
"consequences": [
"missense_variant"
],
"exon_count": 8,
"exon_rank": 8,
"exon_rank_end": null,
"feature": "ENST00000965696.1",
"gene_hgnc_id": 22407,
"gene_symbol": "TMEM106B",
"hgvs_c": "c.754G>A",
"hgvs_p": "p.Asp252Asn",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000635755.1",
"strand": true,
"transcript": "ENST00000965696.1",
"transcript_support_level": null
},
{
"aa_alt": "N",
"aa_end": null,
"aa_length": 274,
"aa_ref": "D",
"aa_start": 252,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2411,
"cdna_start": 1228,
"cds_end": null,
"cds_length": 825,
"cds_start": 754,
"consequences": [
"missense_variant"
],
"exon_count": 8,
"exon_rank": 8,
"exon_rank_end": null,
"feature": "ENST00000965697.1",
"gene_hgnc_id": 22407,
"gene_symbol": "TMEM106B",
"hgvs_c": "c.754G>A",
"hgvs_p": "p.Asp252Asn",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000635756.1",
"strand": true,
"transcript": "ENST00000965697.1",
"transcript_support_level": null
},
{
"aa_alt": "N",
"aa_end": null,
"aa_length": 249,
"aa_ref": "D",
"aa_start": 227,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 6046,
"cdna_start": 815,
"cds_end": null,
"cds_length": 750,
"cds_start": 679,
"consequences": [
"missense_variant"
],
"exon_count": 8,
"exon_rank": 8,
"exon_rank_end": null,
"feature": "ENST00000704417.1",
"gene_hgnc_id": 22407,
"gene_symbol": "TMEM106B",
"hgvs_c": "c.679G>A",
"hgvs_p": "p.Asp227Asn",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000515893.1",
"strand": true,
"transcript": "ENST00000704417.1",
"transcript_support_level": null
},
{
"aa_alt": "N",
"aa_end": null,
"aa_length": 227,
"aa_ref": "D",
"aa_start": 205,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1112,
"cdna_start": 736,
"cds_end": null,
"cds_length": 684,
"cds_start": 613,
"consequences": [
"missense_variant"
],
"exon_count": 7,
"exon_rank": 7,
"exon_rank_end": null,
"feature": "ENST00000704348.1",
"gene_hgnc_id": 22407,
"gene_symbol": "TMEM106B",
"hgvs_c": "c.613G>A",
"hgvs_p": "p.Asp205Asn",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000515859.1",
"strand": true,
"transcript": "ENST00000704348.1",
"transcript_support_level": null
},
{
"aa_alt": "N",
"aa_end": null,
"aa_length": 227,
"aa_ref": "D",
"aa_start": 205,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1051,
"cdna_start": 723,
"cds_end": null,
"cds_length": 684,
"cds_start": 613,
"consequences": [
"missense_variant"
],
"exon_count": 7,
"exon_rank": 7,
"exon_rank_end": null,
"feature": "ENST00000704349.1",
"gene_hgnc_id": 22407,
"gene_symbol": "TMEM106B",
"hgvs_c": "c.613G>A",
"hgvs_p": "p.Asp205Asn",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000515860.1",
"strand": true,
"transcript": "ENST00000704349.1",
"transcript_support_level": null
},
{
"aa_alt": "N",
"aa_end": null,
"aa_length": 227,
"aa_ref": "D",
"aa_start": 205,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2721,
"cdna_start": 935,
"cds_end": null,
"cds_length": 684,
"cds_start": 613,
"consequences": [
"missense_variant"
],
"exon_count": 8,
"exon_rank": 8,
"exon_rank_end": null,
"feature": "ENST00000903750.1",
"gene_hgnc_id": 22407,
"gene_symbol": "TMEM106B",
"hgvs_c": "c.613G>A",
"hgvs_p": "p.Asp205Asn",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000573809.1",
"strand": true,
"transcript": "ENST00000903750.1",
"transcript_support_level": null
},
{
"aa_alt": "N",
"aa_end": null,
"aa_length": 176,
"aa_ref": "D",
"aa_start": 154,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1567,
"cdna_start": 520,
"cds_end": null,
"cds_length": 531,
"cds_start": 460,
"consequences": [
"missense_variant"
],
"exon_count": 6,
"exon_rank": 6,
"exon_rank_end": null,
"feature": "ENST00000704416.1",
"gene_hgnc_id": 22407,
"gene_symbol": "TMEM106B",
"hgvs_c": "c.460G>A",
"hgvs_p": "p.Asp154Asn",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000515892.1",
"strand": true,
"transcript": "ENST00000704416.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 210,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1156,
"cdna_start": null,
"cds_end": null,
"cds_length": 633,
"cds_start": null,
"consequences": [
"3_prime_UTR_variant"
],
"exon_count": 7,
"exon_rank": 7,
"exon_rank_end": null,
"feature": "ENST00000704457.1",
"gene_hgnc_id": 22407,
"gene_symbol": "TMEM106B",
"hgvs_c": "c.*67G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000515907.1",
"strand": true,
"transcript": "ENST00000704457.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "retained_intron",
"canonical": false,
"cdna_end": null,
"cdna_length": 891,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 3,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "ENST00000462754.2",
"gene_hgnc_id": 22407,
"gene_symbol": "TMEM106B",
"hgvs_c": "n.382G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": true,
"transcript": "ENST00000462754.2",
"transcript_support_level": 2
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "nonsense_mediated_decay",
"canonical": false,
"cdna_end": null,
"cdna_length": 823,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 6,
"exon_rank": 6,
"exon_rank_end": null,
"feature": "ENST00000704347.1",
"gene_hgnc_id": 22407,
"gene_symbol": "TMEM106B",
"hgvs_c": "n.*144G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000515858.1",
"strand": true,
"transcript": "ENST00000704347.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "nonsense_mediated_decay",
"canonical": false,
"cdna_end": null,
"cdna_length": 823,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"3_prime_UTR_variant"
],
"exon_count": 6,
"exon_rank": 6,
"exon_rank_end": null,
"feature": "ENST00000704347.1",
"gene_hgnc_id": 22407,
"gene_symbol": "TMEM106B",
"hgvs_c": "n.*144G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000515858.1",
"strand": true,
"transcript": "ENST00000704347.1",
"transcript_support_level": null
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs1554310600",
"effect": "missense_variant",
"frequency_reference_population": null,
"gene_hgnc_id": 22407,
"gene_symbol": "TMEM106B",
"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": "Pathogenic/Likely pathogenic",
"phenotype_combined": "Leukodystrophy, hypomyelinating, 16|not provided",
"phylop100way_prediction": "Pathogenic",
"phylop100way_score": 9.563,
"pos": 12231904,
"ref": "G",
"revel_prediction": "Uncertain_significance",
"revel_score": 0.526,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0,
"transcript": "NM_018374.4"
}
]
}