X-154506862-G-A
Variant names:
Variant summary
Our verdict is Benign. Variant got -17 ACMG points: 0P and 17B. BP4_StrongBP6_Very_StrongBP7BS2
The NM_021806.4(FAM3A):c.642C>T(p.Pro214Pro) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000371 in 1,210,623 control chromosomes in the GnomAD database, including 1 homozygotes. There are 183 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.00027 ( 0 hom., 7 hem., cov: 24)
Exomes 𝑓: 0.00038 ( 1 hom. 176 hem. )
Consequence
FAM3A
NM_021806.4 synonymous
NM_021806.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -2.17
Genes affected
FAM3A (HGNC:13749): (FAM3 metabolism regulating signaling molecule A) This gene encodes a cytokine-like protein. The expression of this gene may be regulated by peroxisome proliferator-activated receptor gamma, and the encoded protein may be involved in the regulation of glucose and lipid metabolism. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Aug 2013]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -17 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.75).
BP6
Variant X-154506862-G-A is Benign according to our data. Variant chrX-154506862-G-A is described in ClinVar as [Benign]. Clinvar id is 736968.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BP7
Synonymous conserved (PhyloP=-2.17 with no splicing effect.
BS2
High Hemizygotes in GnomAd4 at 7 gene
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000274 AC: 31AN: 112942Hom.: 0 Cov.: 24 AF XY: 0.000200 AC XY: 7AN XY: 35080
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GnomAD3 exomes AF: 0.000566 AC: 103AN: 182072Hom.: 0 AF XY: 0.000791 AC XY: 53AN XY: 66986
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GnomAD4 exome AF: 0.000381 AC: 418AN: 1097631Hom.: 1 Cov.: 30 AF XY: 0.000485 AC XY: 176AN XY: 363029
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GnomAD4 genome AF: 0.000274 AC: 31AN: 112992Hom.: 0 Cov.: 24 AF XY: 0.000199 AC XY: 7AN XY: 35140
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ClinVar
Significance: Benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Benign:2
Oct 10, 2018
Labcorp Genetics (formerly Invitae), Labcorp
Significance: Benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing
- -
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Breakthrough Genomics, Breakthrough Genomics
Significance: Benign
Review Status: criteria provided, single submitter
Collection Method: not provided
- -
Computational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at