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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: 1-11790843-G-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=1&pos=11790843&ref=G&alt=C&genome=hg38&allGenes=true"
API Response
json
{
"variants": [
{
"chr": "1",
"pos": 11790843,
"ref": "G",
"alt": "C",
"effect": "missense_variant",
"transcript": "ENST00000376590.9",
"consequences": [
{
"aa_ref": "S",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MTHFR",
"gene_hgnc_id": 7436,
"hgvs_c": "c.1808C>G",
"hgvs_p": "p.Ser603Cys",
"transcript": "NM_005957.5",
"protein_id": "NP_005948.3",
"transcript_support_level": null,
"aa_start": 603,
"aa_end": null,
"aa_length": 656,
"cds_start": 1808,
"cds_end": null,
"cds_length": 1971,
"cdna_start": 1898,
"cdna_end": null,
"cdna_length": 7018,
"mane_select": "ENST00000376590.9",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "C",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MTHFR",
"gene_hgnc_id": 7436,
"hgvs_c": "c.1808C>G",
"hgvs_p": "p.Ser603Cys",
"transcript": "ENST00000376590.9",
"protein_id": "ENSP00000365775.3",
"transcript_support_level": 1,
"aa_start": 603,
"aa_end": null,
"aa_length": 656,
"cds_start": 1808,
"cds_end": null,
"cds_length": 1971,
"cdna_start": 1898,
"cdna_end": null,
"cdna_length": 7018,
"mane_select": "NM_005957.5",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MTHFR",
"gene_hgnc_id": 7436,
"hgvs_c": "c.1928C>G",
"hgvs_p": "p.Ser643Cys",
"transcript": "ENST00000423400.7",
"protein_id": "ENSP00000398908.3",
"transcript_support_level": 1,
"aa_start": 643,
"aa_end": null,
"aa_length": 696,
"cds_start": 1928,
"cds_end": null,
"cds_length": 2091,
"cdna_start": 1940,
"cdna_end": null,
"cdna_length": 2715,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MTHFR",
"gene_hgnc_id": 7436,
"hgvs_c": "c.1808C>G",
"hgvs_p": "p.Ser603Cys",
"transcript": "ENST00000376592.6",
"protein_id": "ENSP00000365777.1",
"transcript_support_level": 1,
"aa_start": 603,
"aa_end": null,
"aa_length": 656,
"cds_start": 1808,
"cds_end": null,
"cds_length": 1971,
"cdna_start": 3258,
"cdna_end": null,
"cdna_length": 8378,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MTHFR",
"gene_hgnc_id": 7436,
"hgvs_c": "c.1931C>G",
"hgvs_p": "p.Ser644Cys",
"transcript": "NM_001330358.2",
"protein_id": "NP_001317287.1",
"transcript_support_level": null,
"aa_start": 644,
"aa_end": null,
"aa_length": 697,
"cds_start": 1931,
"cds_end": null,
"cds_length": 2094,
"cdna_start": 1954,
"cdna_end": null,
"cdna_length": 7074,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MTHFR",
"gene_hgnc_id": 7436,
"hgvs_c": "c.1931C>G",
"hgvs_p": "p.Ser644Cys",
"transcript": "ENST00000376583.7",
"protein_id": "ENSP00000365767.3",
"transcript_support_level": 5,
"aa_start": 644,
"aa_end": null,
"aa_length": 697,
"cds_start": 1931,
"cds_end": null,
"cds_length": 2094,
"cdna_start": 1931,
"cdna_end": null,
"cdna_length": 7044,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MTHFR",
"gene_hgnc_id": 7436,
"hgvs_c": "c.1931C>G",
"hgvs_p": "p.Ser644Cys",
"transcript": "ENST00000376585.6",
"protein_id": "ENSP00000365770.1",
"transcript_support_level": 5,
"aa_start": 644,
"aa_end": null,
"aa_length": 697,
"cds_start": 1931,
"cds_end": null,
"cds_length": 2094,
"cdna_start": 2983,
"cdna_end": null,
"cdna_length": 8094,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MTHFR",
"gene_hgnc_id": 7436,
"hgvs_c": "c.1928C>G",
"hgvs_p": "p.Ser643Cys",
"transcript": "NM_001410750.1",
"protein_id": "NP_001397679.1",
"transcript_support_level": null,
"aa_start": 643,
"aa_end": null,
"aa_length": 696,
"cds_start": 1928,
"cds_end": null,
"cds_length": 2091,
"cdna_start": 1951,
"cdna_end": null,
"cdna_length": 7071,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MTHFR",
"gene_hgnc_id": 7436,
"hgvs_c": "c.1073C>G",
"hgvs_p": "p.Ser358Cys",
"transcript": "ENST00000641820.1",
"protein_id": "ENSP00000492937.1",
"transcript_support_level": null,
"aa_start": 358,
"aa_end": null,
"aa_length": 411,
"cds_start": 1073,
"cds_end": null,
"cds_length": 1236,
"cdna_start": 1368,
"cdna_end": null,
"cdna_length": 1569,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MTHFR",
"gene_hgnc_id": 7436,
"hgvs_c": "c.1808C>G",
"hgvs_p": "p.Ser603Cys",
"transcript": "XM_005263462.5",
"protein_id": "XP_005263519.1",
"transcript_support_level": null,
"aa_start": 603,
"aa_end": null,
"aa_length": 656,
"cds_start": 1808,
"cds_end": null,
"cds_length": 1971,
"cdna_start": 1895,
"cdna_end": null,
"cdna_length": 7015,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MTHFR",
"gene_hgnc_id": 7436,
"hgvs_c": "c.1808C>G",
"hgvs_p": "p.Ser603Cys",
"transcript": "XM_047421178.1",
"protein_id": "XP_047277134.1",
"transcript_support_level": null,
"aa_start": 603,
"aa_end": null,
"aa_length": 656,
"cds_start": 1808,
"cds_end": null,
"cds_length": 1971,
"cdna_start": 2436,
"cdna_end": null,
"cdna_length": 7556,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MTHFR",
"gene_hgnc_id": 7436,
"hgvs_c": "c.1562C>G",
"hgvs_p": "p.Ser521Cys",
"transcript": "XM_005263463.5",
"protein_id": "XP_005263520.1",
"transcript_support_level": null,
"aa_start": 521,
"aa_end": null,
"aa_length": 574,
"cds_start": 1562,
"cds_end": null,
"cds_length": 1725,
"cdna_start": 1678,
"cdna_end": null,
"cdna_length": 6798,
"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": 13,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MTHFR",
"gene_hgnc_id": 7436,
"hgvs_c": "n.*267C>G",
"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,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"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": 11,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MTHFR",
"gene_hgnc_id": 7436,
"hgvs_c": "n.*1320C>G",
"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": 11,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MTHFR",
"gene_hgnc_id": 7436,
"hgvs_c": "n.2177C>G",
"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": [
"3_prime_UTR_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MTHFR",
"gene_hgnc_id": 7436,
"hgvs_c": "n.*267C>G",
"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,
"cds_end": null,
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"cdna_start": null,
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"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": 11,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MTHFR",
"gene_hgnc_id": 7436,
"hgvs_c": "n.*1320C>G",
"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": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": 10,
"intron_rank_end": null,
"gene_symbol": "MTHFR",
"gene_hgnc_id": 7436,
"hgvs_c": "c.1753-127C>G",
"hgvs_p": null,
"transcript": "ENST00000641407.1",
"protein_id": "ENSP00000493098.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 642,
"cds_start": -4,
"cds_end": null,
"cds_length": 1929,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2387,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": 10,
"intron_rank_end": null,
"gene_symbol": "MTHFR",
"gene_hgnc_id": 7436,
"hgvs_c": "n.2270-127C>G",
"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,
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"cdna_start": null,
"cdna_end": null,
"cdna_length": 2945,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
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"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": 11,
"intron_rank_end": null,
"gene_symbol": "MTHFR",
"gene_hgnc_id": 7436,
"hgvs_c": "c.1876-127C>G",
"hgvs_p": null,
"transcript": "XM_011541496.4",
"protein_id": "XP_011539798.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 683,
"cds_start": -4,
"cds_end": null,
"cds_length": 2052,
"cdna_start": null,
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"cdna_length": 6892,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"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": 12,
"intron_rank": 11,
"intron_rank_end": null,
"gene_symbol": "MTHFR",
"gene_hgnc_id": 7436,
"hgvs_c": "c.1873-127C>G",
"hgvs_p": null,
"transcript": "XM_047421174.1",
"protein_id": "XP_047277130.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 682,
"cds_start": -4,
"cds_end": null,
"cds_length": 2049,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 6889,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"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": 12,
"intron_rank": 11,
"intron_rank_end": null,
"gene_symbol": "MTHFR",
"gene_hgnc_id": 7436,
"hgvs_c": "c.1876-95C>G",
"hgvs_p": null,
"transcript": "XM_017001328.3",
"protein_id": "XP_016856817.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 647,
"cds_start": -4,
"cds_end": null,
"cds_length": 1944,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 6924,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"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": 12,
"intron_rank": 11,
"intron_rank_end": null,
"gene_symbol": "MTHFR",
"gene_hgnc_id": 7436,
"hgvs_c": "c.1753-127C>G",
"hgvs_p": null,
"transcript": "XM_047421179.1",
"protein_id": "XP_047277135.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 642,
"cds_start": -4,
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"cds_length": 1929,
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"feature": null
},
{
"aa_ref": null,
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"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": 11,
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"gene_symbol": "MTHFR",
"gene_hgnc_id": 7436,
"hgvs_c": "c.1753-95C>G",
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"transcript": "XM_047421180.1",
"protein_id": "XP_047277136.1",
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"aa_start": null,
"aa_end": null,
"aa_length": 606,
"cds_start": -4,
"cds_end": null,
"cds_length": 1821,
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"cdna_length": 6868,
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"feature": null
},
{
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"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": 11,
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"gene_symbol": "MTHFR",
"gene_hgnc_id": 7436,
"hgvs_c": "c.1753-95C>G",
"hgvs_p": null,
"transcript": "XM_047421181.1",
"protein_id": "XP_047277137.1",
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"aa_start": null,
"aa_end": null,
"aa_length": 606,
"cds_start": -4,
"cds_end": null,
"cds_length": 1821,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 6865,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "MTHFR",
"gene_hgnc_id": 7436,
"dbsnp": "rs758206023",
"frequency_reference_population": 0.000008054572,
"hom_count_reference_population": 0,
"allele_count_reference_population": 13,
"gnomad_exomes_af": 0.00000820855,
"gnomad_genomes_af": 0.00000657462,
"gnomad_exomes_ac": 12,
"gnomad_genomes_ac": 1,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.8071596026420593,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.525,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": 0.1835,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.07,
"bayesdelnoaf_prediction": "Uncertain_significance",
"phylop100way_score": 9.449,
"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": 4,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2,PP3,PP5",
"acmg_by_gene": [
{
"score": 4,
"benign_score": 0,
"pathogenic_score": 4,
"criteria": [
"PM2",
"PP3",
"PP5"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000376590.9",
"gene_symbol": "MTHFR",
"hgnc_id": 7436,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.1808C>G",
"hgvs_p": "p.Ser603Cys"
}
],
"clinvar_disease": "Homocystinuria due to methylene tetrahydrofolate reductase deficiency",
"clinvar_classification": "Pathogenic",
"clinvar_review_status": "no assertion criteria provided",
"clinvar_submissions_summary": "null",
"phenotype_combined": "Homocystinuria due to methylene tetrahydrofolate reductase deficiency",
"pathogenicity_classification_combined": "Pathogenic",
"custom_annotations": null
}
],
"message": null
}