10-87020370-C-T
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_001146157.3(FAM25A):c.46C>T(p.Arg16Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000265 in 1,549,368 control chromosomes in the GnomAD database, including 3 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/18 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R16H) has been classified as Uncertain significance.
Frequency
Consequence
NM_001146157.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000230 AC: 35AN: 152080Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.00165 AC: 253AN: 153638Hom.: 3 AF XY: 0.00141 AC XY: 115AN XY: 81736
GnomAD4 exome AF: 0.000268 AC: 375AN: 1397172Hom.: 3 Cov.: 32 AF XY: 0.000260 AC XY: 179AN XY: 689118
GnomAD4 genome AF: 0.000230 AC: 35AN: 152196Hom.: 0 Cov.: 31 AF XY: 0.000269 AC XY: 20AN XY: 74414
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.46C>T (p.R16C) alteration is located in exon 1 (coding exon 1) of the FAM25A gene. This alteration results from a C to T substitution at nucleotide position 46, causing the arginine (R) at amino acid position 16 to be replaced by a cysteine (C). 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