19-55763152-C-T
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_ModerateBP6_ModerateBS2
The NM_001145014.2(RFPL4A):c.841C>T(p.Pro281Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000041 in 1,536,188 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. 16/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. P281T) has been classified as Uncertain significance.
Frequency
Consequence
NM_001145014.2 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: 0.0000139 AC: 2AN: 144110Hom.: 0 Cov.: 29
GnomAD3 exomes AF: 0.0000195 AC: 3AN: 153794Hom.: 0 AF XY: 0.0000122 AC XY: 1AN XY: 81732
GnomAD4 exome AF: 0.0000438 AC: 61AN: 1392078Hom.: 2 Cov.: 42 AF XY: 0.0000378 AC XY: 26AN XY: 686944
GnomAD4 genome AF: 0.0000139 AC: 2AN: 144110Hom.: 0 Cov.: 29 AF XY: 0.0000142 AC XY: 1AN XY: 70482
ClinVar
Submissions by phenotype
not specified Benign:1
This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at