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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: 2-176328354-A-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=2&pos=176328354&ref=A&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "2",
"pos": 176328354,
"ref": "A",
"alt": "C",
"effect": "missense_variant",
"transcript": "NM_006554.5",
"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": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MTX2",
"gene_hgnc_id": 7506,
"hgvs_c": "c.347A>C",
"hgvs_p": "p.Glu116Ala",
"transcript": "NM_006554.5",
"protein_id": "NP_006545.1",
"transcript_support_level": null,
"aa_start": 116,
"aa_end": null,
"aa_length": 263,
"cds_start": 347,
"cds_end": null,
"cds_length": 792,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000249442.11",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_006554.5"
},
{
"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": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MTX2",
"gene_hgnc_id": 7506,
"hgvs_c": "c.347A>C",
"hgvs_p": "p.Glu116Ala",
"transcript": "ENST00000249442.11",
"protein_id": "ENSP00000249442.6",
"transcript_support_level": 1,
"aa_start": 116,
"aa_end": null,
"aa_length": 263,
"cds_start": 347,
"cds_end": null,
"cds_length": 792,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_006554.5",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000249442.11"
},
{
"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": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MTX2",
"gene_hgnc_id": 7506,
"hgvs_c": "n.*437A>C",
"hgvs_p": null,
"transcript": "ENST00000420864.5",
"protein_id": "ENSP00000403545.1",
"transcript_support_level": 1,
"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": "ENST00000420864.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MTX2",
"gene_hgnc_id": 7506,
"hgvs_c": "n.*437A>C",
"hgvs_p": null,
"transcript": "ENST00000420864.5",
"protein_id": "ENSP00000403545.1",
"transcript_support_level": 1,
"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": "ENST00000420864.5"
},
{
"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": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MTX2",
"gene_hgnc_id": 7506,
"hgvs_c": "c.470A>C",
"hgvs_p": "p.Glu157Ala",
"transcript": "ENST00000926928.1",
"protein_id": "ENSP00000596987.1",
"transcript_support_level": null,
"aa_start": 157,
"aa_end": null,
"aa_length": 304,
"cds_start": 470,
"cds_end": null,
"cds_length": 915,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000926928.1"
},
{
"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": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MTX2",
"gene_hgnc_id": 7506,
"hgvs_c": "c.347A>C",
"hgvs_p": "p.Glu116Ala",
"transcript": "ENST00000954016.1",
"protein_id": "ENSP00000624075.1",
"transcript_support_level": null,
"aa_start": 116,
"aa_end": null,
"aa_length": 263,
"cds_start": 347,
"cds_end": null,
"cds_length": 792,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000954016.1"
},
{
"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": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MTX2",
"gene_hgnc_id": 7506,
"hgvs_c": "c.341A>C",
"hgvs_p": "p.Glu114Ala",
"transcript": "ENST00000894532.1",
"protein_id": "ENSP00000564591.1",
"transcript_support_level": null,
"aa_start": 114,
"aa_end": null,
"aa_length": 261,
"cds_start": 341,
"cds_end": null,
"cds_length": 786,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000894532.1"
},
{
"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": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MTX2",
"gene_hgnc_id": 7506,
"hgvs_c": "c.341A>C",
"hgvs_p": "p.Glu114Ala",
"transcript": "ENST00000926925.1",
"protein_id": "ENSP00000596984.1",
"transcript_support_level": null,
"aa_start": 114,
"aa_end": null,
"aa_length": 261,
"cds_start": 341,
"cds_end": null,
"cds_length": 786,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000926925.1"
},
{
"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": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MTX2",
"gene_hgnc_id": 7506,
"hgvs_c": "c.347A>C",
"hgvs_p": "p.Glu116Ala",
"transcript": "ENST00000926926.1",
"protein_id": "ENSP00000596985.1",
"transcript_support_level": null,
"aa_start": 116,
"aa_end": null,
"aa_length": 259,
"cds_start": 347,
"cds_end": null,
"cds_length": 780,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000926926.1"
},
{
"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": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MTX2",
"gene_hgnc_id": 7506,
"hgvs_c": "c.317A>C",
"hgvs_p": "p.Glu106Ala",
"transcript": "NM_001006635.3",
"protein_id": "NP_001006636.1",
"transcript_support_level": null,
"aa_start": 106,
"aa_end": null,
"aa_length": 253,
"cds_start": 317,
"cds_end": null,
"cds_length": 762,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001006635.3"
},
{
"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": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MTX2",
"gene_hgnc_id": 7506,
"hgvs_c": "c.347A>C",
"hgvs_p": "p.Glu116Ala",
"transcript": "NM_001319097.2",
"protein_id": "NP_001306026.1",
"transcript_support_level": null,
"aa_start": 116,
"aa_end": null,
"aa_length": 240,
"cds_start": 347,
"cds_end": null,
"cds_length": 723,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001319097.2"
},
{
"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": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MTX2",
"gene_hgnc_id": 7506,
"hgvs_c": "c.347A>C",
"hgvs_p": "p.Glu116Ala",
"transcript": "ENST00000452865.1",
"protein_id": "ENSP00000398757.1",
"transcript_support_level": 3,
"aa_start": 116,
"aa_end": null,
"aa_length": 228,
"cds_start": 347,
"cds_end": null,
"cds_length": 689,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000452865.1"
},
{
"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": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MTX2",
"gene_hgnc_id": 7506,
"hgvs_c": "c.227A>C",
"hgvs_p": "p.Glu76Ala",
"transcript": "ENST00000954017.1",
"protein_id": "ENSP00000624076.1",
"transcript_support_level": null,
"aa_start": 76,
"aa_end": null,
"aa_length": 223,
"cds_start": 227,
"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": "ENST00000954017.1"
},
{
"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": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MTX2",
"gene_hgnc_id": 7506,
"hgvs_c": "c.347A>C",
"hgvs_p": "p.Glu116Ala",
"transcript": "ENST00000894533.1",
"protein_id": "ENSP00000564592.1",
"transcript_support_level": null,
"aa_start": 116,
"aa_end": null,
"aa_length": 221,
"cds_start": 347,
"cds_end": null,
"cds_length": 666,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000894533.1"
},
{
"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": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MTX2",
"gene_hgnc_id": 7506,
"hgvs_c": "c.197A>C",
"hgvs_p": "p.Glu66Ala",
"transcript": "ENST00000926927.1",
"protein_id": "ENSP00000596986.1",
"transcript_support_level": null,
"aa_start": 66,
"aa_end": null,
"aa_length": 213,
"cds_start": 197,
"cds_end": null,
"cds_length": 642,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000926927.1"
},
{
"aa_ref": "E",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MTX2",
"gene_hgnc_id": 7506,
"hgvs_c": "c.179A>C",
"hgvs_p": "p.Glu60Ala",
"transcript": "ENST00000443241.5",
"protein_id": "ENSP00000414176.1",
"transcript_support_level": 3,
"aa_start": 60,
"aa_end": null,
"aa_length": 207,
"cds_start": 179,
"cds_end": null,
"cds_length": 624,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000443241.5"
},
{
"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": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MTX2",
"gene_hgnc_id": 7506,
"hgvs_c": "c.347A>C",
"hgvs_p": "p.Glu116Ala",
"transcript": "NM_001319098.2",
"protein_id": "NP_001306027.1",
"transcript_support_level": null,
"aa_start": 116,
"aa_end": null,
"aa_length": 183,
"cds_start": 347,
"cds_end": null,
"cds_length": 552,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001319098.2"
},
{
"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": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MTX2",
"gene_hgnc_id": 7506,
"hgvs_c": "c.317A>C",
"hgvs_p": "p.Glu106Ala",
"transcript": "XM_047442985.1",
"protein_id": "XP_047298941.1",
"transcript_support_level": null,
"aa_start": 106,
"aa_end": null,
"aa_length": 253,
"cds_start": 317,
"cds_end": null,
"cds_length": 762,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047442985.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": 5,
"intron_rank_end": null,
"gene_symbol": "MTX2",
"gene_hgnc_id": 7506,
"hgvs_c": "c.286-520A>C",
"hgvs_p": null,
"transcript": "ENST00000926929.1",
"protein_id": "ENSP00000596988.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 232,
"cds_start": null,
"cds_end": null,
"cds_length": 699,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000926929.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"downstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MTX2",
"gene_hgnc_id": 7506,
"hgvs_c": "n.*334A>C",
"hgvs_p": null,
"transcript": "ENST00000423461.6",
"protein_id": "ENSP00000402204.2",
"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": "ENST00000423461.6"
}
],
"gene_symbol": "MTX2",
"gene_hgnc_id": 7506,
"dbsnp": "rs1024851436",
"frequency_reference_population": 0.000010073119,
"hom_count_reference_population": 0,
"allele_count_reference_population": 16,
"gnomad_exomes_af": 0.00000626181,
"gnomad_genomes_af": 0.0000463263,
"gnomad_exomes_ac": 9,
"gnomad_genomes_ac": 7,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.273139625787735,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.258,
"revel_prediction": "Benign",
"alphamissense_score": 0.4204,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.06,
"bayesdelnoaf_prediction": "Uncertain_significance",
"phylop100way_score": 9.321,
"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": 0,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2,BP4,BS1_Supporting",
"acmg_by_gene": [
{
"score": 0,
"benign_score": 2,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4",
"BS1_Supporting"
],
"verdict": "Uncertain_significance",
"transcript": "NM_006554.5",
"gene_symbol": "MTX2",
"hgnc_id": 7506,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.347A>C",
"hgvs_p": "p.Glu116Ala"
}
],
"clinvar_disease": "not specified",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"phenotype_combined": "not specified",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}