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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: 17-17577005-C-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=17&pos=17577005&ref=C&alt=A&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 2,
"criteria": [
"PM2",
"BP4_Moderate"
],
"effects": [
"missense_variant"
],
"gene_symbol": "PEMT",
"hgnc_id": 8830,
"hgvs_c": "c.119G>T",
"hgvs_p": "p.Arg40Leu",
"inheritance_mode": "AR",
"pathogenic_score": 2,
"score": 0,
"transcript": "NM_148172.3",
"verdict": "Uncertain_significance"
}
],
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2,BP4_Moderate",
"acmg_score": 0,
"allele_count_reference_population": 3,
"alphamissense_prediction": null,
"alphamissense_score": 0.0906,
"alt": "A",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Benign",
"bayesdelnoaf_score": -0.41,
"chr": "17",
"clinvar_classification": "Uncertain significance",
"clinvar_disease": "not specified",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"computational_prediction_selected": "Benign",
"computational_score_selected": 0.222743958234787,
"computational_source_selected": "MetaRNN",
"consequences": [
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 236,
"aa_ref": "R",
"aa_start": 40,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1021,
"cdna_start": 201,
"cds_end": null,
"cds_length": 711,
"cds_start": 119,
"consequences": [
"missense_variant"
],
"exon_count": 7,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "NM_148172.3",
"gene_hgnc_id": 8830,
"gene_symbol": "PEMT",
"hgvs_c": "c.119G>T",
"hgvs_p": "p.Arg40Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000255389.10",
"protein_coding": true,
"protein_id": "NP_680477.1",
"strand": false,
"transcript": "NM_148172.3",
"transcript_support_level": null
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 236,
"aa_ref": "R",
"aa_start": 40,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 1021,
"cdna_start": 201,
"cds_end": null,
"cds_length": 711,
"cds_start": 119,
"consequences": [
"missense_variant"
],
"exon_count": 7,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000255389.10",
"gene_hgnc_id": 8830,
"gene_symbol": "PEMT",
"hgvs_c": "c.119G>T",
"hgvs_p": "p.Arg40Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_148172.3",
"protein_coding": true,
"protein_id": "ENSP00000255389.5",
"strand": false,
"transcript": "ENST00000255389.10",
"transcript_support_level": 1
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 199,
"aa_ref": "R",
"aa_start": 3,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 895,
"cdna_start": 75,
"cds_end": null,
"cds_length": 600,
"cds_start": 8,
"consequences": [
"missense_variant"
],
"exon_count": 7,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000395782.5",
"gene_hgnc_id": 8830,
"gene_symbol": "PEMT",
"hgvs_c": "c.8G>T",
"hgvs_p": "p.Arg3Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000379128.1",
"strand": false,
"transcript": "ENST00000395782.5",
"transcript_support_level": 1
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 199,
"aa_ref": "R",
"aa_start": 3,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1008,
"cdna_start": 188,
"cds_end": null,
"cds_length": 600,
"cds_start": 8,
"consequences": [
"missense_variant"
],
"exon_count": 7,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000395783.5",
"gene_hgnc_id": 8830,
"gene_symbol": "PEMT",
"hgvs_c": "c.8G>T",
"hgvs_p": "p.Arg3Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000379129.1",
"strand": false,
"transcript": "ENST00000395783.5",
"transcript_support_level": 1
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 243,
"aa_ref": "R",
"aa_start": 40,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1012,
"cdna_start": 173,
"cds_end": null,
"cds_length": 732,
"cds_start": 119,
"consequences": [
"missense_variant"
],
"exon_count": 7,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000900344.1",
"gene_hgnc_id": 8830,
"gene_symbol": "PEMT",
"hgvs_c": "c.119G>T",
"hgvs_p": "p.Arg40Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000570403.1",
"strand": false,
"transcript": "ENST00000900344.1",
"transcript_support_level": null
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 235,
"aa_ref": "R",
"aa_start": 40,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1000,
"cdna_start": 185,
"cds_end": null,
"cds_length": 708,
"cds_start": 119,
"consequences": [
"missense_variant"
],
"exon_count": 7,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000900343.1",
"gene_hgnc_id": 8830,
"gene_symbol": "PEMT",
"hgvs_c": "c.119G>T",
"hgvs_p": "p.Arg40Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000570402.1",
"strand": false,
"transcript": "ENST00000900343.1",
"transcript_support_level": null
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 232,
"aa_ref": "R",
"aa_start": 40,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1052,
"cdna_start": 201,
"cds_end": null,
"cds_length": 699,
"cds_start": 119,
"consequences": [
"missense_variant"
],
"exon_count": 8,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "NM_001267552.2",
"gene_hgnc_id": 8830,
"gene_symbol": "PEMT",
"hgvs_c": "c.119G>T",
"hgvs_p": "p.Arg40Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001254481.1",
"strand": false,
"transcript": "NM_001267552.2",
"transcript_support_level": null
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 232,
"aa_ref": "R",
"aa_start": 40,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1050,
"cdna_start": 201,
"cds_end": null,
"cds_length": 699,
"cds_start": 119,
"consequences": [
"missense_variant"
],
"exon_count": 8,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000395781.6",
"gene_hgnc_id": 8830,
"gene_symbol": "PEMT",
"hgvs_c": "c.119G>T",
"hgvs_p": "p.Arg40Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000379127.2",
"strand": false,
"transcript": "ENST00000395781.6",
"transcript_support_level": 2
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 214,
"aa_ref": "R",
"aa_start": 18,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 955,
"cdna_start": 135,
"cds_end": null,
"cds_length": 645,
"cds_start": 53,
"consequences": [
"missense_variant"
],
"exon_count": 7,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "NM_001267551.2",
"gene_hgnc_id": 8830,
"gene_symbol": "PEMT",
"hgvs_c": "c.53G>T",
"hgvs_p": "p.Arg18Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001254480.1",
"strand": false,
"transcript": "NM_001267551.2",
"transcript_support_level": null
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 211,
"aa_ref": "R",
"aa_start": 18,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 960,
"cdna_start": 106,
"cds_end": null,
"cds_length": 636,
"cds_start": 53,
"consequences": [
"missense_variant"
],
"exon_count": 8,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000435340.6",
"gene_hgnc_id": 8830,
"gene_symbol": "PEMT",
"hgvs_c": "c.53G>T",
"hgvs_p": "p.Arg18Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000391288.2",
"strand": false,
"transcript": "ENST00000435340.6",
"transcript_support_level": 5
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 211,
"aa_ref": "R",
"aa_start": 18,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 956,
"cdna_start": 145,
"cds_end": null,
"cds_length": 636,
"cds_start": 53,
"consequences": [
"missense_variant"
],
"exon_count": 7,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000900341.1",
"gene_hgnc_id": 8830,
"gene_symbol": "PEMT",
"hgvs_c": "c.53G>T",
"hgvs_p": "p.Arg18Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000570400.1",
"strand": false,
"transcript": "ENST00000900341.1",
"transcript_support_level": null
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 211,
"aa_ref": "R",
"aa_start": 40,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 932,
"cdna_start": 185,
"cds_end": null,
"cds_length": 636,
"cds_start": 119,
"consequences": [
"missense_variant"
],
"exon_count": 6,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000900342.1",
"gene_hgnc_id": 8830,
"gene_symbol": "PEMT",
"hgvs_c": "c.119G>T",
"hgvs_p": "p.Arg40Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000570401.1",
"strand": false,
"transcript": "ENST00000900342.1",
"transcript_support_level": null
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 199,
"aa_ref": "R",
"aa_start": 3,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1023,
"cdna_start": 203,
"cds_end": null,
"cds_length": 600,
"cds_start": 8,
"consequences": [
"missense_variant"
],
"exon_count": 7,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "NM_007169.3",
"gene_hgnc_id": 8830,
"gene_symbol": "PEMT",
"hgvs_c": "c.8G>T",
"hgvs_p": "p.Arg3Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_009100.2",
"strand": false,
"transcript": "NM_007169.3",
"transcript_support_level": null
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 199,
"aa_ref": "R",
"aa_start": 3,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 926,
"cdna_start": 106,
"cds_end": null,
"cds_length": 600,
"cds_start": 8,
"consequences": [
"missense_variant"
],
"exon_count": 7,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "NM_148173.2",
"gene_hgnc_id": 8830,
"gene_symbol": "PEMT",
"hgvs_c": "c.8G>T",
"hgvs_p": "p.Arg3Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_680478.1",
"strand": false,
"transcript": "NM_148173.2",
"transcript_support_level": null
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 241,
"aa_ref": "R",
"aa_start": 45,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1233,
"cdna_start": 413,
"cds_end": null,
"cds_length": 726,
"cds_start": 134,
"consequences": [
"missense_variant"
],
"exon_count": 7,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "XM_006721418.5",
"gene_hgnc_id": 8830,
"gene_symbol": "PEMT",
"hgvs_c": "c.134G>T",
"hgvs_p": "p.Arg45Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_006721481.3",
"strand": false,
"transcript": "XM_006721418.5",
"transcript_support_level": null
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 199,
"aa_ref": "R",
"aa_start": 3,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1019,
"cdna_start": 199,
"cds_end": null,
"cds_length": 600,
"cds_start": 8,
"consequences": [
"missense_variant"
],
"exon_count": 7,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "XM_024450532.2",
"gene_hgnc_id": 8830,
"gene_symbol": "PEMT",
"hgvs_c": "c.8G>T",
"hgvs_p": "p.Arg3Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_024306300.1",
"strand": false,
"transcript": "XM_024450532.2",
"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": 662,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 6,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000421096.5",
"gene_hgnc_id": 8830,
"gene_symbol": "PEMT",
"hgvs_c": "n.143G>T",
"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": "ENST00000421096.5",
"transcript_support_level": 3
},
{
"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": 591,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 5,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000461404.1",
"gene_hgnc_id": 8830,
"gene_symbol": "PEMT",
"hgvs_c": "n.119G>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000463713.1",
"strand": false,
"transcript": "ENST00000461404.1",
"transcript_support_level": 5
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 473,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 4,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000472446.1",
"gene_hgnc_id": 8830,
"gene_symbol": "PEMT",
"hgvs_c": "n.130G>T",
"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": "ENST00000472446.1",
"transcript_support_level": 3
},
{
"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": 708,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 5,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000580147.5",
"gene_hgnc_id": 8830,
"gene_symbol": "PEMT",
"hgvs_c": "n.119G>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000463112.1",
"strand": false,
"transcript": "ENST00000580147.5",
"transcript_support_level": 3
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs767735937",
"effect": "missense_variant",
"frequency_reference_population": 0.0000020524917,
"gene_hgnc_id": 8830,
"gene_symbol": "PEMT",
"gnomad_exomes_ac": 3,
"gnomad_exomes_af": 0.00000205249,
"gnomad_exomes_homalt": 0,
"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": "Uncertain significance",
"phenotype_combined": "not specified",
"phylop100way_prediction": "Benign",
"phylop100way_score": 0.103,
"pos": 17577005,
"ref": "C",
"revel_prediction": "Benign",
"revel_score": 0.08,
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"splice_source_selected": "max_spliceai",
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"transcript": "NM_148172.3"
}
]
}