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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: 1-11792354-C-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=1&pos=11792354&ref=C&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "1",
"pos": 11792354,
"ref": "C",
"alt": "A",
"effect": "missense_variant",
"transcript": "ENST00000376590.9",
"consequences": [
{
"aa_ref": "R",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MTHFR",
"gene_hgnc_id": 7436,
"hgvs_c": "c.1556G>T",
"hgvs_p": "p.Arg519Leu",
"transcript": "NM_005957.5",
"protein_id": "NP_005948.3",
"transcript_support_level": null,
"aa_start": 519,
"aa_end": null,
"aa_length": 656,
"cds_start": 1556,
"cds_end": null,
"cds_length": 1971,
"cdna_start": 1646,
"cdna_end": null,
"cdna_length": 7018,
"mane_select": "ENST00000376590.9",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "L",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MTHFR",
"gene_hgnc_id": 7436,
"hgvs_c": "c.1556G>T",
"hgvs_p": "p.Arg519Leu",
"transcript": "ENST00000376590.9",
"protein_id": "ENSP00000365775.3",
"transcript_support_level": 1,
"aa_start": 519,
"aa_end": null,
"aa_length": 656,
"cds_start": 1556,
"cds_end": null,
"cds_length": 1971,
"cdna_start": 1646,
"cdna_end": null,
"cdna_length": 7018,
"mane_select": "NM_005957.5",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MTHFR",
"gene_hgnc_id": 7436,
"hgvs_c": "c.1676G>T",
"hgvs_p": "p.Arg559Leu",
"transcript": "ENST00000423400.7",
"protein_id": "ENSP00000398908.3",
"transcript_support_level": 1,
"aa_start": 559,
"aa_end": null,
"aa_length": 696,
"cds_start": 1676,
"cds_end": null,
"cds_length": 2091,
"cdna_start": 1688,
"cdna_end": null,
"cdna_length": 2715,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MTHFR",
"gene_hgnc_id": 7436,
"hgvs_c": "c.1556G>T",
"hgvs_p": "p.Arg519Leu",
"transcript": "ENST00000376592.6",
"protein_id": "ENSP00000365777.1",
"transcript_support_level": 1,
"aa_start": 519,
"aa_end": null,
"aa_length": 656,
"cds_start": 1556,
"cds_end": null,
"cds_length": 1971,
"cdna_start": 3006,
"cdna_end": null,
"cdna_length": 8378,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MTHFR",
"gene_hgnc_id": 7436,
"hgvs_c": "c.1679G>T",
"hgvs_p": "p.Arg560Leu",
"transcript": "NM_001330358.2",
"protein_id": "NP_001317287.1",
"transcript_support_level": null,
"aa_start": 560,
"aa_end": null,
"aa_length": 697,
"cds_start": 1679,
"cds_end": null,
"cds_length": 2094,
"cdna_start": 1702,
"cdna_end": null,
"cdna_length": 7074,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MTHFR",
"gene_hgnc_id": 7436,
"hgvs_c": "c.1679G>T",
"hgvs_p": "p.Arg560Leu",
"transcript": "ENST00000376583.7",
"protein_id": "ENSP00000365767.3",
"transcript_support_level": 5,
"aa_start": 560,
"aa_end": null,
"aa_length": 697,
"cds_start": 1679,
"cds_end": null,
"cds_length": 2094,
"cdna_start": 1679,
"cdna_end": null,
"cdna_length": 7044,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MTHFR",
"gene_hgnc_id": 7436,
"hgvs_c": "c.1679G>T",
"hgvs_p": "p.Arg560Leu",
"transcript": "ENST00000376585.6",
"protein_id": "ENSP00000365770.1",
"transcript_support_level": 5,
"aa_start": 560,
"aa_end": null,
"aa_length": 697,
"cds_start": 1679,
"cds_end": null,
"cds_length": 2094,
"cdna_start": 2731,
"cdna_end": null,
"cdna_length": 8094,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MTHFR",
"gene_hgnc_id": 7436,
"hgvs_c": "c.1676G>T",
"hgvs_p": "p.Arg559Leu",
"transcript": "NM_001410750.1",
"protein_id": "NP_001397679.1",
"transcript_support_level": null,
"aa_start": 559,
"aa_end": null,
"aa_length": 696,
"cds_start": 1676,
"cds_end": null,
"cds_length": 2091,
"cdna_start": 1699,
"cdna_end": null,
"cdna_length": 7071,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MTHFR",
"gene_hgnc_id": 7436,
"hgvs_c": "c.1556G>T",
"hgvs_p": "p.Arg519Leu",
"transcript": "ENST00000641407.1",
"protein_id": "ENSP00000493098.1",
"transcript_support_level": null,
"aa_start": 519,
"aa_end": null,
"aa_length": 642,
"cds_start": 1556,
"cds_end": null,
"cds_length": 1929,
"cdna_start": 1823,
"cdna_end": null,
"cdna_length": 2387,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MTHFR",
"gene_hgnc_id": 7436,
"hgvs_c": "c.821G>T",
"hgvs_p": "p.Arg274Leu",
"transcript": "ENST00000641820.1",
"protein_id": "ENSP00000492937.1",
"transcript_support_level": null,
"aa_start": 274,
"aa_end": null,
"aa_length": 411,
"cds_start": 821,
"cds_end": null,
"cds_length": 1236,
"cdna_start": 1116,
"cdna_end": null,
"cdna_length": 1569,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MTHFR",
"gene_hgnc_id": 7436,
"hgvs_c": "c.1679G>T",
"hgvs_p": "p.Arg560Leu",
"transcript": "XM_011541496.4",
"protein_id": "XP_011539798.1",
"transcript_support_level": null,
"aa_start": 560,
"aa_end": null,
"aa_length": 683,
"cds_start": 1679,
"cds_end": null,
"cds_length": 2052,
"cdna_start": 1702,
"cdna_end": null,
"cdna_length": 6892,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MTHFR",
"gene_hgnc_id": 7436,
"hgvs_c": "c.1676G>T",
"hgvs_p": "p.Arg559Leu",
"transcript": "XM_047421174.1",
"protein_id": "XP_047277130.1",
"transcript_support_level": null,
"aa_start": 559,
"aa_end": null,
"aa_length": 682,
"cds_start": 1676,
"cds_end": null,
"cds_length": 2049,
"cdna_start": 1699,
"cdna_end": null,
"cdna_length": 6889,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MTHFR",
"gene_hgnc_id": 7436,
"hgvs_c": "c.1556G>T",
"hgvs_p": "p.Arg519Leu",
"transcript": "XM_005263462.5",
"protein_id": "XP_005263519.1",
"transcript_support_level": null,
"aa_start": 519,
"aa_end": null,
"aa_length": 656,
"cds_start": 1556,
"cds_end": null,
"cds_length": 1971,
"cdna_start": 1643,
"cdna_end": null,
"cdna_length": 7015,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MTHFR",
"gene_hgnc_id": 7436,
"hgvs_c": "c.1556G>T",
"hgvs_p": "p.Arg519Leu",
"transcript": "XM_047421178.1",
"protein_id": "XP_047277134.1",
"transcript_support_level": null,
"aa_start": 519,
"aa_end": null,
"aa_length": 656,
"cds_start": 1556,
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"cdna_start": 2184,
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"cdna_length": 7556,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MTHFR",
"gene_hgnc_id": 7436,
"hgvs_c": "c.1679G>T",
"hgvs_p": "p.Arg560Leu",
"transcript": "XM_017001328.3",
"protein_id": "XP_016856817.1",
"transcript_support_level": null,
"aa_start": 560,
"aa_end": null,
"aa_length": 647,
"cds_start": 1679,
"cds_end": null,
"cds_length": 1944,
"cdna_start": 1702,
"cdna_end": null,
"cdna_length": 6924,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MTHFR",
"gene_hgnc_id": 7436,
"hgvs_c": "c.1556G>T",
"hgvs_p": "p.Arg519Leu",
"transcript": "XM_047421179.1",
"protein_id": "XP_047277135.1",
"transcript_support_level": null,
"aa_start": 519,
"aa_end": null,
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"cds_start": 1556,
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"cdna_start": 1646,
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"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MTHFR",
"gene_hgnc_id": 7436,
"hgvs_c": "c.1556G>T",
"hgvs_p": "p.Arg519Leu",
"transcript": "XM_047421180.1",
"protein_id": "XP_047277136.1",
"transcript_support_level": null,
"aa_start": 519,
"aa_end": null,
"aa_length": 606,
"cds_start": 1556,
"cds_end": null,
"cds_length": 1821,
"cdna_start": 1646,
"cdna_end": null,
"cdna_length": 6868,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MTHFR",
"gene_hgnc_id": 7436,
"hgvs_c": "c.1556G>T",
"hgvs_p": "p.Arg519Leu",
"transcript": "XM_047421181.1",
"protein_id": "XP_047277137.1",
"transcript_support_level": null,
"aa_start": 519,
"aa_end": null,
"aa_length": 606,
"cds_start": 1556,
"cds_end": null,
"cds_length": 1821,
"cdna_start": 1643,
"cdna_end": null,
"cdna_length": 6865,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MTHFR",
"gene_hgnc_id": 7436,
"hgvs_c": "c.1310G>T",
"hgvs_p": "p.Arg437Leu",
"transcript": "XM_005263463.5",
"protein_id": "XP_005263520.1",
"transcript_support_level": null,
"aa_start": 437,
"aa_end": null,
"aa_length": 574,
"cds_start": 1310,
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"cdna_start": 1426,
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"mane_select": null,
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"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MTHFR",
"gene_hgnc_id": 7436,
"hgvs_c": "n.1556G>T",
"hgvs_p": null,
"transcript": "ENST00000641446.1",
"protein_id": "ENSP00000493262.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
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"cdna_start": null,
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"cdna_length": 2820,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MTHFR",
"gene_hgnc_id": 7436,
"hgvs_c": "n.*1068G>T",
"hgvs_p": null,
"transcript": "ENST00000641747.1",
"protein_id": "ENSP00000493116.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 3227,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MTHFR",
"gene_hgnc_id": 7436,
"hgvs_c": "n.1925G>T",
"hgvs_p": null,
"transcript": "ENST00000641759.1",
"protein_id": null,
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2454,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MTHFR",
"gene_hgnc_id": 7436,
"hgvs_c": "n.2073G>T",
"hgvs_p": null,
"transcript": "ENST00000641805.1",
"protein_id": null,
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2945,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MTHFR",
"gene_hgnc_id": 7436,
"hgvs_c": "n.*1068G>T",
"hgvs_p": null,
"transcript": "ENST00000641747.1",
"protein_id": "ENSP00000493116.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 3227,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "MTHFR",
"gene_hgnc_id": 7436,
"dbsnp": "rs45449298",
"frequency_reference_population": 0.0004479243,
"hom_count_reference_population": 7,
"allele_count_reference_population": 723,
"gnomad_exomes_af": 0.000378303,
"gnomad_genomes_af": 0.00111607,
"gnomad_exomes_ac": 553,
"gnomad_genomes_ac": 170,
"gnomad_exomes_homalt": 3,
"gnomad_genomes_homalt": 4,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.009096026420593262,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.20999999344348907,
"splice_prediction_selected": "Uncertain_significance",
"splice_source_selected": "max_spliceai",
"revel_score": 0.095,
"revel_prediction": "Benign",
"alphamissense_score": 0.1364,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.28,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 4.482,
"phylop100way_prediction": "Uncertain_significance",
"spliceai_max_score": 0.21,
"spliceai_max_prediction": "Uncertain_significance",
"dbscsnv_ada_score": null,
"dbscsnv_ada_prediction": null,
"apogee2_score": null,
"apogee2_prediction": null,
"mitotip_score": null,
"mitotip_prediction": null,
"acmg_score": -5,
"acmg_classification": "Likely_benign",
"acmg_criteria": "BS1_Supporting,BS2",
"acmg_by_gene": [
{
"score": -5,
"benign_score": 5,
"pathogenic_score": 0,
"criteria": [
"BS1_Supporting",
"BS2"
],
"verdict": "Likely_benign",
"transcript": "ENST00000376590.9",
"gene_symbol": "MTHFR",
"hgnc_id": 7436,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.1556G>T",
"hgvs_p": "p.Arg519Leu"
}
],
"clinvar_disease": " folate-sensitive,Homocystinuria due to methylene tetrahydrofolate reductase deficiency,MTHFR-related disorder,Neural tube defects,Schizophrenia,Thrombophilia due to thrombin defect,not provided",
"clinvar_classification": "Conflicting classifications of pathogenicity",
"clinvar_review_status": "criteria provided, conflicting classifications",
"clinvar_submissions_summary": "US:4 B:1",
"phenotype_combined": "not provided|Homocystinuria due to methylene tetrahydrofolate reductase deficiency;Thrombophilia due to thrombin defect;Neural tube defects, folate-sensitive;Schizophrenia|MTHFR-related disorder|Homocystinuria due to methylene tetrahydrofolate reductase deficiency",
"pathogenicity_classification_combined": "Conflicting classifications of pathogenicity",
"custom_annotations": null
}
],
"message": null
}