1-152410178-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_016190.3(CRNN):c.904G>A(p.Val302Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000018 in 1,608,038 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_016190.3 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: 0.0000342 AC: 5AN: 146344Hom.: 0 Cov.: 30
GnomAD3 exomes AF: 0.0000318 AC: 8AN: 251416Hom.: 0 AF XY: 0.0000294 AC XY: 4AN XY: 135870
GnomAD4 exome AF: 0.0000164 AC: 24AN: 1461694Hom.: 0 Cov.: 32 AF XY: 0.0000151 AC XY: 11AN XY: 727156
GnomAD4 genome AF: 0.0000342 AC: 5AN: 146344Hom.: 0 Cov.: 30 AF XY: 0.0000563 AC XY: 4AN XY: 71044
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.904G>A (p.V302M) alteration is located in exon 3 (coding exon 2) of the CRNN gene. This alteration results from a G to A substitution at nucleotide position 904, causing the valine (V) at amino acid position 302 to be replaced by a methionine (M). 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