chr3-184338418-G-T
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Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_144635.5(FAM131A):c.120G>T(p.Trp40Cys) variant causes a missense change. The variant allele was found at a frequency of 0.00000875 in 1,485,118 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: 𝑓 0.000013 ( 0 hom., cov: 33)
Exomes 𝑓: 0.0000083 ( 0 hom. )
Consequence
FAM131A
NM_144635.5 missense
NM_144635.5 missense
Scores
4
8
5
Clinical Significance
Conservation
PhyloP100: 5.34
Genes affected
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 2 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
FAM131A | NM_144635.5 | c.120G>T | p.Trp40Cys | missense_variant | 2/6 | ENST00000383847.7 | NP_653236.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
FAM131A | ENST00000383847.7 | c.120G>T | p.Trp40Cys | missense_variant | 2/6 | 2 | NM_144635.5 | ENSP00000373360 | A1 |
Frequencies
GnomAD3 genomes AF: 0.0000131 AC: 2AN: 152208Hom.: 0 Cov.: 33
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GnomAD4 exome AF: 0.00000825 AC: 11AN: 1332910Hom.: 0 Cov.: 30 AF XY: 0.00000919 AC XY: 6AN XY: 653178
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GnomAD4 genome AF: 0.0000131 AC: 2AN: 152208Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 74360
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ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Sep 16, 2021 | The c.120G>T (p.W40C) alteration is located in exon 2 (coding exon 2) of the FAM131A gene. This alteration results from a G to T substitution at nucleotide position 120, causing the tryptophan (W) at amino acid position 40 to be replaced by a cysteine (C). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Pathogenic
BayesDel_addAF
Uncertain
T
BayesDel_noAF
Benign
CADD
Pathogenic
DANN
Uncertain
Eigen
Uncertain
Eigen_PC
Uncertain
FATHMM_MKL
Uncertain
D
LIST_S2
Benign
T;T
M_CAP
Uncertain
D
MetaRNN
Uncertain
D;D
MetaSVM
Benign
T
MutationTaster
Benign
D;D;D;D;D
PrimateAI
Pathogenic
D
PROVEAN
Uncertain
.;D
REVEL
Benign
Sift
Pathogenic
.;D
Sift4G
Pathogenic
.;D
Vest4
0.62
MutPred
Gain of disorder (P = 0.0509);Gain of disorder (P = 0.0509);
MVP
0.35
MPC
1.5
ClinPred
D
GERP RS
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Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at