3-184344792-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_144635.5(FAM131A):c.923C>T(p.Ser308Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00011 in 1,612,284 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_144635.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
FAM131A | NM_144635.5 | c.923C>T | p.Ser308Leu | missense_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.923C>T | p.Ser308Leu | missense_variant | 6/6 | 2 | NM_144635.5 | ENSP00000373360 | A1 |
Frequencies
GnomAD3 genomes AF: 0.0000854 AC: 13AN: 152248Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000113 AC: 28AN: 247206Hom.: 0 AF XY: 0.000156 AC XY: 21AN XY: 134348
GnomAD4 exome AF: 0.000112 AC: 164AN: 1459918Hom.: 1 Cov.: 32 AF XY: 0.000139 AC XY: 101AN XY: 726382
GnomAD4 genome AF: 0.0000853 AC: 13AN: 152366Hom.: 0 Cov.: 33 AF XY: 0.0000671 AC XY: 5AN XY: 74512
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jul 26, 2022 | The c.923C>T (p.S308L) alteration is located in exon 6 (coding exon 6) of the FAM131A gene. This alteration results from a C to T substitution at nucleotide position 923, causing the serine (S) at amino acid position 308 to be replaced by a leucine (L). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at