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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: X-15324758-T-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=X&pos=15324758&ref=T&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "X",
"pos": 15324758,
"ref": "T",
"alt": "C",
"effect": "synonymous_variant",
"transcript": "ENST00000333590.6",
"consequences": [
{
"aa_ref": "Q",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PIGA",
"gene_hgnc_id": 8957,
"hgvs_c": "c.1095A>G",
"hgvs_p": "p.Gln365Gln",
"transcript": "NM_002641.4",
"protein_id": "NP_002632.1",
"transcript_support_level": null,
"aa_start": 365,
"aa_end": null,
"aa_length": 484,
"cds_start": 1095,
"cds_end": null,
"cds_length": 1455,
"cdna_start": 1180,
"cdna_end": null,
"cdna_length": 3590,
"mane_select": "ENST00000333590.6",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Q",
"aa_alt": "Q",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PIGA",
"gene_hgnc_id": 8957,
"hgvs_c": "c.1095A>G",
"hgvs_p": "p.Gln365Gln",
"transcript": "ENST00000333590.6",
"protein_id": "ENSP00000369820.3",
"transcript_support_level": 1,
"aa_start": 365,
"aa_end": null,
"aa_length": 484,
"cds_start": 1095,
"cds_end": null,
"cds_length": 1455,
"cdna_start": 1180,
"cdna_end": null,
"cdna_length": 3590,
"mane_select": "NM_002641.4",
"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": 2,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "PIGA",
"gene_hgnc_id": 8957,
"hgvs_c": "c.81+262A>G",
"hgvs_p": null,
"transcript": "ENST00000475746.1",
"protein_id": "ENSP00000488970.1",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 50,
"cds_start": -4,
"cds_end": null,
"cds_length": 153,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 153,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Q",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PIGA",
"gene_hgnc_id": 8957,
"hgvs_c": "c.1188A>G",
"hgvs_p": "p.Gln396Gln",
"transcript": "NM_001440789.1",
"protein_id": "NP_001427718.1",
"transcript_support_level": null,
"aa_start": 396,
"aa_end": null,
"aa_length": 515,
"cds_start": 1188,
"cds_end": null,
"cds_length": 1548,
"cdna_start": 1273,
"cdna_end": null,
"cdna_length": 3683,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Q",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PIGA",
"gene_hgnc_id": 8957,
"hgvs_c": "c.1095A>G",
"hgvs_p": "p.Gln365Gln",
"transcript": "ENST00000542278.6",
"protein_id": "ENSP00000442653.2",
"transcript_support_level": 5,
"aa_start": 365,
"aa_end": null,
"aa_length": 484,
"cds_start": 1095,
"cds_end": null,
"cds_length": 1455,
"cdna_start": 1215,
"cdna_end": null,
"cdna_length": 3626,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Q",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PIGA",
"gene_hgnc_id": 8957,
"hgvs_c": "c.588A>G",
"hgvs_p": "p.Gln196Gln",
"transcript": "ENST00000482148.6",
"protein_id": "ENSP00000489528.1",
"transcript_support_level": 5,
"aa_start": 196,
"aa_end": null,
"aa_length": 315,
"cds_start": 588,
"cds_end": null,
"cds_length": 948,
"cdna_start": 653,
"cdna_end": null,
"cdna_length": 1092,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Q",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PIGA",
"gene_hgnc_id": 8957,
"hgvs_c": "c.486A>G",
"hgvs_p": "p.Gln162Gln",
"transcript": "NM_001440790.1",
"protein_id": "NP_001427719.1",
"transcript_support_level": null,
"aa_start": 162,
"aa_end": null,
"aa_length": 281,
"cds_start": 486,
"cds_end": null,
"cds_length": 846,
"cdna_start": 496,
"cdna_end": null,
"cdna_length": 2906,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Q",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PIGA",
"gene_hgnc_id": 8957,
"hgvs_c": "c.393A>G",
"hgvs_p": "p.Gln131Gln",
"transcript": "NM_020473.3",
"protein_id": "NP_065206.3",
"transcript_support_level": null,
"aa_start": 131,
"aa_end": null,
"aa_length": 250,
"cds_start": 393,
"cds_end": null,
"cds_length": 753,
"cdna_start": 434,
"cdna_end": null,
"cdna_length": 2849,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Q",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PIGA",
"gene_hgnc_id": 8957,
"hgvs_c": "c.393A>G",
"hgvs_p": "p.Gln131Gln",
"transcript": "ENST00000634582.1",
"protein_id": "ENSP00000489540.1",
"transcript_support_level": 2,
"aa_start": 131,
"aa_end": null,
"aa_length": 250,
"cds_start": 393,
"cds_end": null,
"cds_length": 753,
"cdna_start": 424,
"cdna_end": null,
"cdna_length": 965,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Q",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PIGA",
"gene_hgnc_id": 8957,
"hgvs_c": "c.150A>G",
"hgvs_p": "p.Gln50Gln",
"transcript": "ENST00000637296.1",
"protein_id": "ENSP00000490545.1",
"transcript_support_level": 5,
"aa_start": 50,
"aa_end": null,
"aa_length": 169,
"cds_start": 150,
"cds_end": null,
"cds_length": 510,
"cdna_start": 606,
"cdna_end": null,
"cdna_length": 2113,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Q",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PIGA",
"gene_hgnc_id": 8957,
"hgvs_c": "c.150A>G",
"hgvs_p": "p.Gln50Gln",
"transcript": "ENST00000634640.1",
"protein_id": "ENSP00000489083.1",
"transcript_support_level": 5,
"aa_start": 50,
"aa_end": null,
"aa_length": 149,
"cds_start": 150,
"cds_end": null,
"cds_length": 451,
"cdna_start": 553,
"cdna_end": null,
"cdna_length": 854,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Q",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PIGA",
"gene_hgnc_id": 8957,
"hgvs_c": "c.402A>G",
"hgvs_p": "p.Gln134Gln",
"transcript": "XM_011545539.3",
"protein_id": "XP_011543841.1",
"transcript_support_level": null,
"aa_start": 134,
"aa_end": null,
"aa_length": 253,
"cds_start": 402,
"cds_end": null,
"cds_length": 762,
"cdna_start": 2807,
"cdna_end": null,
"cdna_length": 5222,
"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": 2,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PIGA",
"gene_hgnc_id": 8957,
"hgvs_c": "n.367A>G",
"hgvs_p": null,
"transcript": "ENST00000463173.1",
"protein_id": null,
"transcript_support_level": 3,
"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": 520,
"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": 4,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PIGA",
"gene_hgnc_id": 8957,
"hgvs_c": "n.1328A>G",
"hgvs_p": null,
"transcript": "ENST00000635045.1",
"protein_id": null,
"transcript_support_level": 2,
"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": 3738,
"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": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PIGA",
"gene_hgnc_id": 8957,
"hgvs_c": "n.717A>G",
"hgvs_p": null,
"transcript": "ENST00000635480.1",
"protein_id": null,
"transcript_support_level": 3,
"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": 743,
"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": 5,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PIGA",
"gene_hgnc_id": 8957,
"hgvs_c": "n.*364A>G",
"hgvs_p": null,
"transcript": "ENST00000635598.1",
"protein_id": "ENSP00000489207.1",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
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"cdna_length": 3246,
"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": 4,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PIGA",
"gene_hgnc_id": 8957,
"hgvs_c": "n.436A>G",
"hgvs_p": null,
"transcript": "ENST00000635631.1",
"protein_id": null,
"transcript_support_level": 5,
"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": 2850,
"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": 6,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PIGA",
"gene_hgnc_id": 8957,
"hgvs_c": "n.*576A>G",
"hgvs_p": null,
"transcript": "ENST00000637626.1",
"protein_id": "ENSP00000489928.1",
"transcript_support_level": 5,
"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": 3877,
"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": 5,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PIGA",
"gene_hgnc_id": 8957,
"hgvs_c": "n.*356A>G",
"hgvs_p": null,
"transcript": "ENST00000638131.1",
"protein_id": "ENSP00000490483.1",
"transcript_support_level": 5,
"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": 2963,
"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": 5,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PIGA",
"gene_hgnc_id": 8957,
"hgvs_c": "n.837A>G",
"hgvs_p": null,
"transcript": "NR_033835.1",
"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": 3252,
"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": 5,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PIGA",
"gene_hgnc_id": 8957,
"hgvs_c": "n.553A>G",
"hgvs_p": null,
"transcript": "NR_033836.1",
"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,
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"cdna_length": 2968,
"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": 6,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PIGA",
"gene_hgnc_id": 8957,
"hgvs_c": "n.899A>G",
"hgvs_p": null,
"transcript": "NR_199789.1",
"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": 3309,
"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": 6,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PIGA",
"gene_hgnc_id": 8957,
"hgvs_c": "n.615A>G",
"hgvs_p": null,
"transcript": "NR_199790.1",
"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,
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"mane_select": null,
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},
{
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},
{
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},
{
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"gene_symbol": "PIGA",
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},
{
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"strand": true,
"consequences": [
"downstream_gene_variant"
],
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"gene_symbol": "PIGA",
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"transcript": "ENST00000634286.1",
"protein_id": "ENSP00000489491.1",
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}
],
"gene_symbol": "PIGA",
"gene_hgnc_id": 8957,
"dbsnp": "rs1555944375",
"frequency_reference_population": null,
"hom_count_reference_population": 0,
"allele_count_reference_population": 0,
"gnomad_exomes_af": 9.14239e-7,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": 1,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": 0,
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"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": -0.8999999761581421,
"computational_prediction_selected": "Benign",
"computational_source_selected": "BayesDel_noAF",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.9,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 0.792,
"phylop100way_prediction": "Benign",
"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": -5,
"acmg_classification": "Likely_benign",
"acmg_criteria": "PM2,BP4_Strong,BP6_Moderate,BP7",
"acmg_by_gene": [
{
"score": -5,
"benign_score": 7,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4_Strong",
"BP6_Moderate",
"BP7"
],
"verdict": "Likely_benign",
"transcript": "ENST00000333590.6",
"gene_symbol": "PIGA",
"hgnc_id": 8957,
"effects": [
"synonymous_variant"
],
"inheritance_mode": "Unknown,XL,AD",
"hgvs_c": "c.1095A>G",
"hgvs_p": "p.Gln365Gln"
}
],
"clinvar_disease": "Multiple congenital anomalies-hypotonia-seizures syndrome 2",
"clinvar_classification": "Likely benign",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "LB:1",
"phenotype_combined": "Multiple congenital anomalies-hypotonia-seizures syndrome 2",
"pathogenicity_classification_combined": "Likely benign",
"custom_annotations": null
}
],
"message": null
}