9-131260979-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_033387.4(FAM78A):c.695G>A(p.Arg232Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000105 in 1,613,116 control chromosomes in the GnomAD database, with no homozygous occurrence. 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_033387.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000789 AC: 12AN: 152154Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000686 AC: 17AN: 247736Hom.: 0 AF XY: 0.0000821 AC XY: 11AN XY: 134020
GnomAD4 exome AF: 0.000107 AC: 157AN: 1460844Hom.: 0 Cov.: 31 AF XY: 0.000103 AC XY: 75AN XY: 726666
GnomAD4 genome AF: 0.0000788 AC: 12AN: 152272Hom.: 0 Cov.: 33 AF XY: 0.0000537 AC XY: 4AN XY: 74450
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.695G>A (p.R232Q) alteration is located in exon 2 (coding exon 2) of the FAM78A gene. This alteration results from a G to A substitution at nucleotide position 695, causing the arginine (R) at amino acid position 232 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