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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: 4-140461967-A-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=4&pos=140461967&ref=A&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "4",
"pos": 140461967,
"ref": "A",
"alt": "T",
"effect": "missense_variant",
"transcript": "NM_001277353.2",
"consequences": [
{
"aa_ref": "L",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MGAT4D",
"gene_hgnc_id": 43619,
"hgvs_c": "c.724T>A",
"hgvs_p": "p.Leu242Met",
"transcript": "NM_001277353.2",
"protein_id": "NP_001264282.1",
"transcript_support_level": null,
"aa_start": 242,
"aa_end": null,
"aa_length": 374,
"cds_start": 724,
"cds_end": null,
"cds_length": 1125,
"cdna_start": 795,
"cdna_end": null,
"cdna_length": 2370,
"mane_select": "ENST00000511113.6",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001277353.2"
},
{
"aa_ref": "L",
"aa_alt": "M",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MGAT4D",
"gene_hgnc_id": 43619,
"hgvs_c": "c.724T>A",
"hgvs_p": "p.Leu242Met",
"transcript": "ENST00000511113.6",
"protein_id": "ENSP00000421185.1",
"transcript_support_level": 5,
"aa_start": 242,
"aa_end": null,
"aa_length": 374,
"cds_start": 724,
"cds_end": null,
"cds_length": 1125,
"cdna_start": 795,
"cdna_end": null,
"cdna_length": 2370,
"mane_select": "NM_001277353.2",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000511113.6"
},
{
"aa_ref": "L",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MGAT4D",
"gene_hgnc_id": 43619,
"hgvs_c": "c.724T>A",
"hgvs_p": "p.Leu242Met",
"transcript": "ENST00000503109.6",
"protein_id": "ENSP00000426225.2",
"transcript_support_level": 5,
"aa_start": 242,
"aa_end": null,
"aa_length": 375,
"cds_start": 724,
"cds_end": null,
"cds_length": 1128,
"cdna_start": 724,
"cdna_end": null,
"cdna_length": 1281,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000503109.6"
},
{
"aa_ref": "L",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MGAT4D",
"gene_hgnc_id": 43619,
"hgvs_c": "c.724T>A",
"hgvs_p": "p.Leu242Met",
"transcript": "XM_011531650.4",
"protein_id": "XP_011529952.1",
"transcript_support_level": null,
"aa_start": 242,
"aa_end": null,
"aa_length": 364,
"cds_start": 724,
"cds_end": null,
"cds_length": 1095,
"cdna_start": 795,
"cdna_end": null,
"cdna_length": 2340,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_011531650.4"
},
{
"aa_ref": "L",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MGAT4D",
"gene_hgnc_id": 43619,
"hgvs_c": "c.676T>A",
"hgvs_p": "p.Leu226Met",
"transcript": "XM_011531651.3",
"protein_id": "XP_011529953.1",
"transcript_support_level": null,
"aa_start": 226,
"aa_end": null,
"aa_length": 358,
"cds_start": 676,
"cds_end": null,
"cds_length": 1077,
"cdna_start": 1052,
"cdna_end": null,
"cdna_length": 2627,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_011531651.3"
},
{
"aa_ref": "L",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MGAT4D",
"gene_hgnc_id": 43619,
"hgvs_c": "c.676T>A",
"hgvs_p": "p.Leu226Met",
"transcript": "XM_011531652.3",
"protein_id": "XP_011529954.1",
"transcript_support_level": null,
"aa_start": 226,
"aa_end": null,
"aa_length": 358,
"cds_start": 676,
"cds_end": null,
"cds_length": 1077,
"cdna_start": 1053,
"cdna_end": null,
"cdna_length": 2628,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_011531652.3"
},
{
"aa_ref": "L",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MGAT4D",
"gene_hgnc_id": 43619,
"hgvs_c": "c.676T>A",
"hgvs_p": "p.Leu226Met",
"transcript": "XM_011531653.4",
"protein_id": "XP_011529955.1",
"transcript_support_level": null,
"aa_start": 226,
"aa_end": null,
"aa_length": 358,
"cds_start": 676,
"cds_end": null,
"cds_length": 1077,
"cdna_start": 1002,
"cdna_end": null,
"cdna_length": 2577,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_011531653.4"
},
{
"aa_ref": "L",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MGAT4D",
"gene_hgnc_id": 43619,
"hgvs_c": "c.724T>A",
"hgvs_p": "p.Leu242Met",
"transcript": "XM_011531654.4",
"protein_id": "XP_011529956.1",
"transcript_support_level": null,
"aa_start": 242,
"aa_end": null,
"aa_length": 355,
"cds_start": 724,
"cds_end": null,
"cds_length": 1068,
"cdna_start": 795,
"cdna_end": null,
"cdna_length": 2313,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_011531654.4"
},
{
"aa_ref": "L",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MGAT4D",
"gene_hgnc_id": 43619,
"hgvs_c": "c.586T>A",
"hgvs_p": "p.Leu196Met",
"transcript": "XM_011531656.4",
"protein_id": "XP_011529958.1",
"transcript_support_level": null,
"aa_start": 196,
"aa_end": null,
"aa_length": 328,
"cds_start": 586,
"cds_end": null,
"cds_length": 987,
"cdna_start": 657,
"cdna_end": null,
"cdna_length": 2232,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_011531656.4"
},
{
"aa_ref": "L",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MGAT4D",
"gene_hgnc_id": 43619,
"hgvs_c": "c.580T>A",
"hgvs_p": "p.Leu194Met",
"transcript": "XM_011531657.4",
"protein_id": "XP_011529959.1",
"transcript_support_level": null,
"aa_start": 194,
"aa_end": null,
"aa_length": 326,
"cds_start": 580,
"cds_end": null,
"cds_length": 981,
"cdna_start": 651,
"cdna_end": null,
"cdna_length": 2226,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_011531657.4"
},
{
"aa_ref": "L",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MGAT4D",
"gene_hgnc_id": 43619,
"hgvs_c": "c.427T>A",
"hgvs_p": "p.Leu143Met",
"transcript": "XM_011531658.4",
"protein_id": "XP_011529960.1",
"transcript_support_level": null,
"aa_start": 143,
"aa_end": null,
"aa_length": 275,
"cds_start": 427,
"cds_end": null,
"cds_length": 828,
"cdna_start": 498,
"cdna_end": null,
"cdna_length": 2073,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_011531658.4"
},
{
"aa_ref": "L",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MGAT4D",
"gene_hgnc_id": 43619,
"hgvs_c": "c.724T>A",
"hgvs_p": "p.Leu242Met",
"transcript": "XM_011531659.3",
"protein_id": "XP_011529961.1",
"transcript_support_level": null,
"aa_start": 242,
"aa_end": null,
"aa_length": 262,
"cds_start": 724,
"cds_end": null,
"cds_length": 789,
"cdna_start": 795,
"cdna_end": null,
"cdna_length": 921,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_011531659.3"
},
{
"aa_ref": "L",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MGAT4D",
"gene_hgnc_id": 43619,
"hgvs_c": "c.166T>A",
"hgvs_p": "p.Leu56Met",
"transcript": "XM_011531664.3",
"protein_id": "XP_011529966.1",
"transcript_support_level": null,
"aa_start": 56,
"aa_end": null,
"aa_length": 188,
"cds_start": 166,
"cds_end": null,
"cds_length": 567,
"cdna_start": 616,
"cdna_end": null,
"cdna_length": 2191,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_011531664.3"
},
{
"aa_ref": "L",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MGAT4D",
"gene_hgnc_id": 43619,
"hgvs_c": "c.166T>A",
"hgvs_p": "p.Leu56Met",
"transcript": "XM_011531665.4",
"protein_id": "XP_011529967.1",
"transcript_support_level": null,
"aa_start": 56,
"aa_end": null,
"aa_length": 188,
"cds_start": 166,
"cds_end": null,
"cds_length": 567,
"cdna_start": 364,
"cdna_end": null,
"cdna_length": 1939,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_011531665.4"
},
{
"aa_ref": "L",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MGAT4D",
"gene_hgnc_id": 43619,
"hgvs_c": "c.166T>A",
"hgvs_p": "p.Leu56Met",
"transcript": "XM_047449648.1",
"protein_id": "XP_047305604.1",
"transcript_support_level": null,
"aa_start": 56,
"aa_end": null,
"aa_length": 188,
"cds_start": 166,
"cds_end": null,
"cds_length": 567,
"cdna_start": 276,
"cdna_end": null,
"cdna_length": 1851,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047449648.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "MGAT4D",
"gene_hgnc_id": 43619,
"hgvs_c": "c.254-5248T>A",
"hgvs_p": null,
"transcript": "ENST00000515354.5",
"protein_id": "ENSP00000423767.1",
"transcript_support_level": 3,
"aa_start": null,
"aa_end": null,
"aa_length": 166,
"cds_start": null,
"cds_end": null,
"cds_length": 501,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1806,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000515354.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": 6,
"intron_rank_end": null,
"gene_symbol": "MGAT4D",
"gene_hgnc_id": 43619,
"hgvs_c": "c.686+2929T>A",
"hgvs_p": null,
"transcript": "XM_011531661.3",
"protein_id": "XP_011529963.1",
"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": 844,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_011531661.3"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": 5,
"intron_rank_end": null,
"gene_symbol": "MGAT4D",
"gene_hgnc_id": 43619,
"hgvs_c": "c.573-5248T>A",
"hgvs_p": null,
"transcript": "XM_011531662.3",
"protein_id": "XP_011529964.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 194,
"cds_start": null,
"cds_end": null,
"cds_length": 585,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 719,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_011531662.3"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MGAT4D",
"gene_hgnc_id": 43619,
"hgvs_c": "n.587T>A",
"hgvs_p": null,
"transcript": "ENST00000513106.5",
"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": 3783,
"mane_select": null,
"mane_plus": null,
"biotype": "retained_intron",
"feature": "ENST00000513106.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MGAT4D",
"gene_hgnc_id": 43619,
"hgvs_c": "n.*135T>A",
"hgvs_p": null,
"transcript": "ENST00000515121.5",
"protein_id": "ENSP00000425945.1",
"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": 810,
"mane_select": null,
"mane_plus": null,
"biotype": "nonsense_mediated_decay",
"feature": "ENST00000515121.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MGAT4D",
"gene_hgnc_id": 43619,
"hgvs_c": "n.979T>A",
"hgvs_p": null,
"transcript": "XR_938697.3",
"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": 1105,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "XR_938697.3"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MGAT4D",
"gene_hgnc_id": 43619,
"hgvs_c": "n.*135T>A",
"hgvs_p": null,
"transcript": "ENST00000515121.5",
"protein_id": "ENSP00000425945.1",
"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": 810,
"mane_select": null,
"mane_plus": null,
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{
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"intron_variant"
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"biotype": "pseudogene",
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],
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"gnomad_genomes_homalt": 4902,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.006428152322769165,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.029999999329447746,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.065,
"revel_prediction": "Benign",
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"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.53,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 4.751,
"phylop100way_prediction": "Uncertain_significance",
"spliceai_max_score": 0.03,
"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": -12,
"acmg_classification": "Benign",
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"acmg_by_gene": [
{
"score": -12,
"benign_score": 12,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BA1"
],
"verdict": "Benign",
"transcript": "NM_001277353.2",
"gene_symbol": "MGAT4D",
"hgnc_id": 43619,
"effects": [
"missense_variant"
],
"inheritance_mode": "",
"hgvs_c": "c.724T>A",
"hgvs_p": "p.Leu242Met"
}
],
"clinvar_disease": "",
"clinvar_classification": "",
"clinvar_review_status": "",
"clinvar_submissions_summary": "",
"phenotype_combined": null,
"pathogenicity_classification_combined": null,
"custom_annotations": null
}
],
"message": null
}