6-2765992-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_020135.3(WRNIP1):c.370C>T(p.Pro124Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000202 in 1,383,664 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/21 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. P124L) has been classified as Uncertain significance.
Frequency
Consequence
NM_020135.3 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: 0.0000396 AC: 6AN: 151588Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000710 AC: 3AN: 42230Hom.: 0 AF XY: 0.0000791 AC XY: 2AN XY: 25288
GnomAD4 exome AF: 0.0000179 AC: 22AN: 1232076Hom.: 0 Cov.: 33 AF XY: 0.0000149 AC XY: 9AN XY: 602294
GnomAD4 genome AF: 0.0000396 AC: 6AN: 151588Hom.: 0 Cov.: 32 AF XY: 0.0000405 AC XY: 3AN XY: 74052
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.370C>T (p.P124S) alteration is located in exon 1 (coding exon 1) of the WRNIP1 gene. This alteration results from a C to T substitution at nucleotide position 370, causing the proline (P) at amino acid position 124 to be replaced by a serine (S). 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