chr3-184344868-A-C
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Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6BP7
The NM_144635.5(FAM131A):āc.999A>Cā(p.Pro333=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000013 in 1,611,030 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (no stars).
Frequency
Genomes: š 0.000020 ( 0 hom., cov: 33)
Exomes š: 0.000012 ( 0 hom. )
Consequence
FAM131A
NM_144635.5 synonymous
NM_144635.5 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.521
Genes affected
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -4 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.81).
BP6
Variant 3-184344868-A-C is Benign according to our data. Variant chr3-184344868-A-C is described in ClinVar as [Likely_benign]. Clinvar id is 3055718.Status of the report is no_assertion_criteria_provided, 0 stars.
BP7
Synonymous conserved (PhyloP=-0.521 with no splicing effect.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
FAM131A | NM_144635.5 | c.999A>C | p.Pro333= | synonymous_variant | 6/6 | ENST00000383847.7 | NP_653236.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
FAM131A | ENST00000383847.7 | c.999A>C | p.Pro333= | synonymous_variant | 6/6 | 2 | NM_144635.5 | ENSP00000373360 | A1 |
Frequencies
GnomAD3 genomes AF: 0.0000197 AC: 3AN: 152174Hom.: 0 Cov.: 33
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GnomAD3 exomes AF: 0.000102 AC: 25AN: 245766Hom.: 0 AF XY: 0.0000747 AC XY: 10AN XY: 133808
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GnomAD4 exome AF: 0.0000123 AC: 18AN: 1458856Hom.: 0 Cov.: 32 AF XY: 0.0000110 AC XY: 8AN XY: 725926
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GnomAD4 genome AF: 0.0000197 AC: 3AN: 152174Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 74344
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: no assertion criteria provided
LINK: link
Submissions by phenotype
FAM131A-related disorder Benign:1
Likely benign, no assertion criteria provided | clinical testing | PreventionGenetics, part of Exact Sciences | Aug 09, 2019 | This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
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Benign
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Benign
DANN
Benign
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