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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: 5-1801442-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=5&pos=1801442&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 9,
"criteria": [
"BP4_Strong",
"BP6",
"BS1"
],
"effects": [
"missense_variant"
],
"gene_symbol": "NDUFS6",
"hgnc_id": 7713,
"hgvs_c": "c.25C>T",
"hgvs_p": "p.Arg9Trp",
"inheritance_mode": "AR",
"pathogenic_score": 0,
"score": -9,
"transcript": "NM_004553.6",
"verdict": "Benign"
},
{
"benign_score": 5,
"criteria": [
"BP4_Strong",
"BP6"
],
"effects": [
"intron_variant"
],
"gene_symbol": "MRPL36",
"hgnc_id": 14490,
"hgvs_c": "c.-13+521G>A",
"hgvs_p": null,
"inheritance_mode": "AR",
"pathogenic_score": 0,
"score": -5,
"transcript": "ENST00000933972.1",
"verdict": "Likely_benign"
}
],
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6,BS1",
"acmg_score": -9,
"allele_count_reference_population": 159,
"alphamissense_prediction": null,
"alphamissense_score": 0.182,
"alt": "T",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Benign",
"bayesdelnoaf_score": -0.3,
"chr": "5",
"clinvar_classification": "Conflicting classifications of pathogenicity",
"clinvar_disease": " nuclear type 1,Mitochondrial complex I deficiency,not provided",
"clinvar_review_status": "criteria provided, conflicting classifications",
"clinvar_submissions_summary": "US:1 LB:1",
"computational_prediction_selected": "Benign",
"computational_score_selected": 0.008570730686187744,
"computational_source_selected": "MetaRNN",
"consequences": [
{
"aa_alt": "W",
"aa_end": null,
"aa_length": 124,
"aa_ref": "R",
"aa_start": 9,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 518,
"cdna_start": 36,
"cds_end": null,
"cds_length": 375,
"cds_start": 25,
"consequences": [
"missense_variant"
],
"exon_count": 4,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "NM_004553.6",
"gene_hgnc_id": 7713,
"gene_symbol": "NDUFS6",
"hgvs_c": "c.25C>T",
"hgvs_p": "p.Arg9Trp",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000274137.10",
"protein_coding": true,
"protein_id": "NP_004544.1",
"strand": true,
"transcript": "NM_004553.6",
"transcript_support_level": null
},
{
"aa_alt": "W",
"aa_end": null,
"aa_length": 124,
"aa_ref": "R",
"aa_start": 9,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 518,
"cdna_start": 36,
"cds_end": null,
"cds_length": 375,
"cds_start": 25,
"consequences": [
"missense_variant"
],
"exon_count": 4,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "ENST00000274137.10",
"gene_hgnc_id": 7713,
"gene_symbol": "NDUFS6",
"hgvs_c": "c.25C>T",
"hgvs_p": "p.Arg9Trp",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_004553.6",
"protein_coding": true,
"protein_id": "ENSP00000274137.6",
"strand": true,
"transcript": "ENST00000274137.10",
"transcript_support_level": 1
},
{
"aa_alt": "W",
"aa_end": null,
"aa_length": 224,
"aa_ref": "R",
"aa_start": 9,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 821,
"cdna_start": 36,
"cds_end": null,
"cds_length": 675,
"cds_start": 25,
"consequences": [
"missense_variant"
],
"exon_count": 4,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "ENST00000933864.1",
"gene_hgnc_id": 7713,
"gene_symbol": "NDUFS6",
"hgvs_c": "c.25C>T",
"hgvs_p": "p.Arg9Trp",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000603923.1",
"strand": true,
"transcript": "ENST00000933864.1",
"transcript_support_level": null
},
{
"aa_alt": "W",
"aa_end": null,
"aa_length": 172,
"aa_ref": "R",
"aa_start": 9,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 550,
"cdna_start": 28,
"cds_end": null,
"cds_length": 519,
"cds_start": 25,
"consequences": [
"missense_variant"
],
"exon_count": 3,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "ENST00000469176.1",
"gene_hgnc_id": 7713,
"gene_symbol": "NDUFS6",
"hgvs_c": "c.25C>T",
"hgvs_p": "p.Arg9Trp",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000422557.1",
"strand": true,
"transcript": "ENST00000469176.1",
"transcript_support_level": 2
},
{
"aa_alt": "W",
"aa_end": null,
"aa_length": 164,
"aa_ref": "R",
"aa_start": 9,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 654,
"cdna_start": 49,
"cds_end": null,
"cds_length": 495,
"cds_start": 25,
"consequences": [
"missense_variant"
],
"exon_count": 4,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "ENST00000933862.1",
"gene_hgnc_id": 7713,
"gene_symbol": "NDUFS6",
"hgvs_c": "c.25C>T",
"hgvs_p": "p.Arg9Trp",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000603921.1",
"strand": true,
"transcript": "ENST00000933862.1",
"transcript_support_level": null
},
{
"aa_alt": "W",
"aa_end": null,
"aa_length": 130,
"aa_ref": "R",
"aa_start": 9,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 583,
"cdna_start": 80,
"cds_end": null,
"cds_length": 393,
"cds_start": 25,
"consequences": [
"missense_variant"
],
"exon_count": 4,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "ENST00000933860.1",
"gene_hgnc_id": 7713,
"gene_symbol": "NDUFS6",
"hgvs_c": "c.25C>T",
"hgvs_p": "p.Arg9Trp",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000603919.1",
"strand": true,
"transcript": "ENST00000933860.1",
"transcript_support_level": null
},
{
"aa_alt": "W",
"aa_end": null,
"aa_length": 118,
"aa_ref": "R",
"aa_start": 9,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 513,
"cdna_start": 49,
"cds_end": null,
"cds_length": 357,
"cds_start": 25,
"consequences": [
"missense_variant"
],
"exon_count": 4,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "ENST00000933863.1",
"gene_hgnc_id": 7713,
"gene_symbol": "NDUFS6",
"hgvs_c": "c.25C>T",
"hgvs_p": "p.Arg9Trp",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000603922.1",
"strand": true,
"transcript": "ENST00000933863.1",
"transcript_support_level": null
},
{
"aa_alt": "W",
"aa_end": null,
"aa_length": 109,
"aa_ref": "R",
"aa_start": 9,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 489,
"cdna_start": 51,
"cds_end": null,
"cds_length": 330,
"cds_start": 25,
"consequences": [
"missense_variant"
],
"exon_count": 4,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "ENST00000870776.1",
"gene_hgnc_id": 7713,
"gene_symbol": "NDUFS6",
"hgvs_c": "c.25C>T",
"hgvs_p": "p.Arg9Trp",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000540835.1",
"strand": true,
"transcript": "ENST00000870776.1",
"transcript_support_level": null
},
{
"aa_alt": "W",
"aa_end": null,
"aa_length": 106,
"aa_ref": "R",
"aa_start": 9,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 465,
"cdna_start": 37,
"cds_end": null,
"cds_length": 321,
"cds_start": 25,
"consequences": [
"missense_variant"
],
"exon_count": 3,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "ENST00000933865.1",
"gene_hgnc_id": 7713,
"gene_symbol": "NDUFS6",
"hgvs_c": "c.25C>T",
"hgvs_p": "p.Arg9Trp",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000603924.1",
"strand": true,
"transcript": "ENST00000933865.1",
"transcript_support_level": null
},
{
"aa_alt": "W",
"aa_end": null,
"aa_length": 83,
"aa_ref": "R",
"aa_start": 9,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 421,
"cdna_start": 59,
"cds_end": null,
"cds_length": 252,
"cds_start": 25,
"consequences": [
"missense_variant"
],
"exon_count": 3,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "ENST00000933861.1",
"gene_hgnc_id": 7713,
"gene_symbol": "NDUFS6",
"hgvs_c": "c.25C>T",
"hgvs_p": "p.Arg9Trp",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000603920.1",
"strand": true,
"transcript": "ENST00000933861.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 103,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 600,
"cdna_start": null,
"cds_end": null,
"cds_length": 312,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 2,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000933972.1",
"gene_hgnc_id": 14490,
"gene_symbol": "MRPL36",
"hgvs_c": "c.-13+521G>A",
"hgvs_p": null,
"intron_rank": 1,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000604031.1",
"strand": false,
"transcript": "ENST00000933972.1",
"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": 260,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 2,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "ENST00000510329.1",
"gene_hgnc_id": 7713,
"gene_symbol": "NDUFS6",
"hgvs_c": "n.22C>T",
"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": "ENST00000510329.1",
"transcript_support_level": 3
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 103,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 595,
"cdna_start": null,
"cds_end": null,
"cds_length": 312,
"cds_start": null,
"consequences": [
"upstream_gene_variant"
],
"exon_count": 2,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000505818.1",
"gene_hgnc_id": 14490,
"gene_symbol": "MRPL36",
"hgvs_c": "c.-121G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000427152.1",
"strand": true,
"transcript": "ENST00000505818.1",
"transcript_support_level": 3
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 103,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1567,
"cdna_start": null,
"cds_end": null,
"cds_length": 312,
"cds_start": null,
"consequences": [
"upstream_gene_variant"
],
"exon_count": 2,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000887752.1",
"gene_hgnc_id": 14490,
"gene_symbol": "MRPL36",
"hgvs_c": "c.-1096G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000557811.1",
"strand": true,
"transcript": "ENST00000887752.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 103,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 675,
"cdna_start": null,
"cds_end": null,
"cds_length": 312,
"cds_start": null,
"consequences": [
"upstream_gene_variant"
],
"exon_count": 2,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000887753.1",
"gene_hgnc_id": 14490,
"gene_symbol": "MRPL36",
"hgvs_c": "c.-217G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000557812.1",
"strand": true,
"transcript": "ENST00000887753.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 103,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 601,
"cdna_start": null,
"cds_end": null,
"cds_length": 312,
"cds_start": null,
"consequences": [
"upstream_gene_variant"
],
"exon_count": 2,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000887754.1",
"gene_hgnc_id": 14490,
"gene_symbol": "MRPL36",
"hgvs_c": "c.-194G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000557813.1",
"strand": true,
"transcript": "ENST00000887754.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 118,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 664,
"cdna_start": null,
"cds_end": null,
"cds_length": 357,
"cds_start": null,
"consequences": [
"upstream_gene_variant"
],
"exon_count": 2,
"exon_rank": null,
"exon_rank_end": null,
"feature": "XM_011514080.3",
"gene_hgnc_id": 14490,
"gene_symbol": "MRPL36",
"hgvs_c": "c.-76G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_011512382.1",
"strand": true,
"transcript": "XM_011514080.3",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 103,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 628,
"cdna_start": null,
"cds_end": null,
"cds_length": 312,
"cds_start": null,
"consequences": [
"upstream_gene_variant"
],
"exon_count": 2,
"exon_rank": null,
"exon_rank_end": null,
"feature": "XM_017009751.3",
"gene_hgnc_id": 14490,
"gene_symbol": "MRPL36",
"hgvs_c": "c.-217G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_016865240.1",
"strand": true,
"transcript": "XM_017009751.3",
"transcript_support_level": null
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs376509886",
"effect": "missense_variant",
"frequency_reference_population": 0.000099055054,
"gene_hgnc_id": 7713,
"gene_symbol": "NDUFS6",
"gnomad_exomes_ac": 143,
"gnomad_exomes_af": 0.0000984317,
"gnomad_exomes_homalt": 1,
"gnomad_genomes_ac": 16,
"gnomad_genomes_af": 0.000104998,
"gnomad_genomes_homalt": 0,
"gnomad_mito_heteroplasmic": null,
"gnomad_mito_homoplasmic": null,
"hom_count_reference_population": 1,
"mitotip_prediction": null,
"mitotip_score": null,
"pathogenicity_classification_combined": "Conflicting classifications of pathogenicity",
"phenotype_combined": "Mitochondrial complex I deficiency, nuclear type 1|not provided|Mitochondrial complex I deficiency",
"phylop100way_prediction": "Benign",
"phylop100way_score": 0.282,
"pos": 1801442,
"ref": "C",
"revel_prediction": "Benign",
"revel_score": 0.225,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0,
"transcript": "NM_004553.6"
}
]
}