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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: 1-39965490-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=1&pos=39965490&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "1",
"pos": 39965490,
"ref": "C",
"alt": "T",
"effect": "missense_variant",
"transcript": "NM_001136493.3",
"consequences": [
{
"aa_ref": "S",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MFSD2A",
"gene_hgnc_id": 25897,
"hgvs_c": "c.497C>T",
"hgvs_p": "p.Ser166Leu",
"transcript": "NM_032793.5",
"protein_id": "NP_116182.2",
"transcript_support_level": null,
"aa_start": 166,
"aa_end": null,
"aa_length": 530,
"cds_start": 497,
"cds_end": null,
"cds_length": 1593,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000372811.10",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_032793.5"
},
{
"aa_ref": "S",
"aa_alt": "L",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MFSD2A",
"gene_hgnc_id": 25897,
"hgvs_c": "c.497C>T",
"hgvs_p": "p.Ser166Leu",
"transcript": "ENST00000372811.10",
"protein_id": "ENSP00000361898.6",
"transcript_support_level": 1,
"aa_start": 166,
"aa_end": null,
"aa_length": 530,
"cds_start": 497,
"cds_end": null,
"cds_length": 1593,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_032793.5",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000372811.10"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MFSD2A",
"gene_hgnc_id": 25897,
"hgvs_c": "n.632C>T",
"hgvs_p": null,
"transcript": "ENST00000483824.5",
"protein_id": null,
"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": "pseudogene",
"feature": "ENST00000483824.5"
},
{
"aa_ref": "S",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MFSD2A",
"gene_hgnc_id": 25897,
"hgvs_c": "c.536C>T",
"hgvs_p": "p.Ser179Leu",
"transcript": "NM_001136493.3",
"protein_id": "NP_001129965.1",
"transcript_support_level": null,
"aa_start": 179,
"aa_end": null,
"aa_length": 543,
"cds_start": 536,
"cds_end": null,
"cds_length": 1632,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001136493.3"
},
{
"aa_ref": "S",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MFSD2A",
"gene_hgnc_id": 25897,
"hgvs_c": "c.536C>T",
"hgvs_p": "p.Ser179Leu",
"transcript": "ENST00000372809.5",
"protein_id": "ENSP00000361895.5",
"transcript_support_level": 2,
"aa_start": 179,
"aa_end": null,
"aa_length": 543,
"cds_start": 536,
"cds_end": null,
"cds_length": 1632,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000372809.5"
},
{
"aa_ref": "S",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MFSD2A",
"gene_hgnc_id": 25897,
"hgvs_c": "c.521C>T",
"hgvs_p": "p.Ser174Leu",
"transcript": "ENST00000857592.1",
"protein_id": "ENSP00000527651.1",
"transcript_support_level": null,
"aa_start": 174,
"aa_end": null,
"aa_length": 538,
"cds_start": 521,
"cds_end": null,
"cds_length": 1617,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000857592.1"
},
{
"aa_ref": "S",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MFSD2A",
"gene_hgnc_id": 25897,
"hgvs_c": "c.491C>T",
"hgvs_p": "p.Ser164Leu",
"transcript": "NM_001349821.2",
"protein_id": "NP_001336750.1",
"transcript_support_level": null,
"aa_start": 164,
"aa_end": null,
"aa_length": 528,
"cds_start": 491,
"cds_end": null,
"cds_length": 1587,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001349821.2"
},
{
"aa_ref": "S",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MFSD2A",
"gene_hgnc_id": 25897,
"hgvs_c": "c.491C>T",
"hgvs_p": "p.Ser164Leu",
"transcript": "ENST00000918782.1",
"protein_id": "ENSP00000588841.1",
"transcript_support_level": null,
"aa_start": 164,
"aa_end": null,
"aa_length": 526,
"cds_start": 491,
"cds_end": null,
"cds_length": 1581,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000918782.1"
},
{
"aa_ref": "S",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MFSD2A",
"gene_hgnc_id": 25897,
"hgvs_c": "c.497C>T",
"hgvs_p": "p.Ser166Leu",
"transcript": "NM_001349822.2",
"protein_id": "NP_001336751.1",
"transcript_support_level": null,
"aa_start": 166,
"aa_end": null,
"aa_length": 502,
"cds_start": 497,
"cds_end": null,
"cds_length": 1509,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001349822.2"
},
{
"aa_ref": "S",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MFSD2A",
"gene_hgnc_id": 25897,
"hgvs_c": "c.497C>T",
"hgvs_p": "p.Ser166Leu",
"transcript": "ENST00000857591.1",
"protein_id": "ENSP00000527650.1",
"transcript_support_level": null,
"aa_start": 166,
"aa_end": null,
"aa_length": 502,
"cds_start": 497,
"cds_end": null,
"cds_length": 1509,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000857591.1"
},
{
"aa_ref": "S",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MFSD2A",
"gene_hgnc_id": 25897,
"hgvs_c": "c.497C>T",
"hgvs_p": "p.Ser166Leu",
"transcript": "ENST00000942984.1",
"protein_id": "ENSP00000613043.1",
"transcript_support_level": null,
"aa_start": 166,
"aa_end": null,
"aa_length": 502,
"cds_start": 497,
"cds_end": null,
"cds_length": 1509,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000942984.1"
},
{
"aa_ref": "S",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MFSD2A",
"gene_hgnc_id": 25897,
"hgvs_c": "c.386C>T",
"hgvs_p": "p.Ser129Leu",
"transcript": "NM_001287809.2",
"protein_id": "NP_001274738.1",
"transcript_support_level": null,
"aa_start": 129,
"aa_end": null,
"aa_length": 491,
"cds_start": 386,
"cds_end": null,
"cds_length": 1476,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001287809.2"
},
{
"aa_ref": "S",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MFSD2A",
"gene_hgnc_id": 25897,
"hgvs_c": "c.497C>T",
"hgvs_p": "p.Ser166Leu",
"transcript": "ENST00000857590.1",
"protein_id": "ENSP00000527649.1",
"transcript_support_level": null,
"aa_start": 166,
"aa_end": null,
"aa_length": 431,
"cds_start": 497,
"cds_end": null,
"cds_length": 1296,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000857590.1"
},
{
"aa_ref": "S",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MFSD2A",
"gene_hgnc_id": 25897,
"hgvs_c": "c.491C>T",
"hgvs_p": "p.Ser164Leu",
"transcript": "ENST00000942985.1",
"protein_id": "ENSP00000613044.1",
"transcript_support_level": null,
"aa_start": 164,
"aa_end": null,
"aa_length": 429,
"cds_start": 491,
"cds_end": null,
"cds_length": 1290,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000942985.1"
},
{
"aa_ref": "S",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MFSD2A",
"gene_hgnc_id": 25897,
"hgvs_c": "c.152C>T",
"hgvs_p": "p.Ser51Leu",
"transcript": "NM_001349823.2",
"protein_id": "NP_001336752.1",
"transcript_support_level": null,
"aa_start": 51,
"aa_end": null,
"aa_length": 415,
"cds_start": 152,
"cds_end": null,
"cds_length": 1248,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001349823.2"
},
{
"aa_ref": "S",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MFSD2A",
"gene_hgnc_id": 25897,
"hgvs_c": "c.29C>T",
"hgvs_p": "p.Ser10Leu",
"transcript": "NM_001287808.2",
"protein_id": "NP_001274737.1",
"transcript_support_level": null,
"aa_start": 10,
"aa_end": null,
"aa_length": 374,
"cds_start": 29,
"cds_end": null,
"cds_length": 1125,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001287808.2"
},
{
"aa_ref": "S",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MFSD2A",
"gene_hgnc_id": 25897,
"hgvs_c": "c.29C>T",
"hgvs_p": "p.Ser10Leu",
"transcript": "ENST00000420632.6",
"protein_id": "ENSP00000391261.2",
"transcript_support_level": 2,
"aa_start": 10,
"aa_end": null,
"aa_length": 374,
"cds_start": 29,
"cds_end": null,
"cds_length": 1125,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000420632.6"
},
{
"aa_ref": "S",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MFSD2A",
"gene_hgnc_id": 25897,
"hgvs_c": "c.491C>T",
"hgvs_p": "p.Ser164Leu",
"transcript": "ENST00000434861.5",
"protein_id": "ENSP00000407606.1",
"transcript_support_level": 3,
"aa_start": 164,
"aa_end": null,
"aa_length": 265,
"cds_start": 491,
"cds_end": null,
"cds_length": 799,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000434861.5"
},
{
"aa_ref": "S",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MFSD2A",
"gene_hgnc_id": 25897,
"hgvs_c": "c.491C>T",
"hgvs_p": "p.Ser164Leu",
"transcript": "XM_047432490.1",
"protein_id": "XP_047288446.1",
"transcript_support_level": null,
"aa_start": 164,
"aa_end": null,
"aa_length": 500,
"cds_start": 491,
"cds_end": null,
"cds_length": 1503,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047432490.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MFSD2A",
"gene_hgnc_id": 25897,
"hgvs_c": "n.409C>T",
"hgvs_p": null,
"transcript": "ENST00000469745.5",
"protein_id": null,
"transcript_support_level": 5,
"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": "ENST00000469745.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MFSD2A",
"gene_hgnc_id": 25897,
"hgvs_c": "n.1144C>T",
"hgvs_p": null,
"transcript": "ENST00000480630.5",
"protein_id": null,
"transcript_support_level": 2,
"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": "ENST00000480630.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MFSD2A",
"gene_hgnc_id": 25897,
"hgvs_c": "n.645C>T",
"hgvs_p": null,
"transcript": "NR_109896.2",
"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": "NR_109896.2"
}
],
"gene_symbol": "MFSD2A",
"gene_hgnc_id": 25897,
"dbsnp": "rs1057517689",
"frequency_reference_population": 0.0000068155177,
"hom_count_reference_population": 0,
"allele_count_reference_population": 11,
"gnomad_exomes_af": 0.0000068406,
"gnomad_genomes_af": 0.00000657445,
"gnomad_exomes_ac": 10,
"gnomad_genomes_ac": 1,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.714678168296814,
"computational_prediction_selected": "Uncertain_significance",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.05999999865889549,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.721,
"revel_prediction": "Pathogenic",
"alphamissense_score": 0.5582,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.35,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 7.56,
"phylop100way_prediction": "Pathogenic",
"spliceai_max_score": 0.06,
"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": 3,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2,PP5",
"acmg_by_gene": [
{
"score": 3,
"benign_score": 0,
"pathogenic_score": 3,
"criteria": [
"PM2",
"PP5"
],
"verdict": "Uncertain_significance",
"transcript": "NM_001136493.3",
"gene_symbol": "MFSD2A",
"hgnc_id": 25897,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.536C>T",
"hgvs_p": "p.Ser179Leu"
}
],
"clinvar_disease": " autosomal recessive, primary,Microcephaly 15,not provided",
"clinvar_classification": "Conflicting classifications of pathogenicity",
"clinvar_review_status": "criteria provided, conflicting classifications",
"clinvar_submissions_summary": "LP:1 US:1",
"phenotype_combined": "Microcephaly 15, primary, autosomal recessive|not provided",
"pathogenicity_classification_combined": "Conflicting classifications of pathogenicity",
"custom_annotations": null
}
],
"message": null
}