chr3-184344891-G-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_144635.5(FAM131A):c.1022G>A(p.Arg341Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000547 in 1,609,202 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/21 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.1022G>A | p.Arg341Gln | 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.1022G>A | p.Arg341Gln | missense_variant | 6/6 | 2 | NM_144635.5 | ENSP00000373360 | A1 |
Frequencies
GnomAD3 genomes AF: 0.0000394 AC: 6AN: 152224Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000132 AC: 32AN: 241974Hom.: 0 AF XY: 0.000159 AC XY: 21AN XY: 132258
GnomAD4 exome AF: 0.0000556 AC: 81AN: 1456860Hom.: 1 Cov.: 32 AF XY: 0.0000814 AC XY: 59AN XY: 725020
GnomAD4 genome AF: 0.0000459 AC: 7AN: 152342Hom.: 0 Cov.: 33 AF XY: 0.0000940 AC XY: 7AN XY: 74498
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Mar 25, 2024 | The c.1022G>A (p.R341Q) alteration is located in exon 6 (coding exon 6) of the FAM131A gene. This alteration results from a G to A substitution at nucleotide position 1022, causing the arginine (R) at amino acid position 341 to be replaced by a glutamine (Q). 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