chr2-233032792-C-T
Variant summary
Our verdict is Likely pathogenic. Variant got 6 ACMG points: 6P and 0B. PM2PP3_Strong
The NM_005383.2(NEU2):c.121C>T(p.Arg41Trp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000229 in 1,614,218 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic 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. R41Q) has been classified as Likely benign.
Frequency
Consequence
NM_005383.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_pathogenic. Variant got 6 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000591 AC: 9AN: 152262Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000756 AC: 19AN: 251178Hom.: 0 AF XY: 0.0000957 AC XY: 13AN XY: 135824
GnomAD4 exome AF: 0.0000192 AC: 28AN: 1461838Hom.: 0 Cov.: 32 AF XY: 0.0000179 AC XY: 13AN XY: 727210
GnomAD4 genome AF: 0.0000591 AC: 9AN: 152380Hom.: 0 Cov.: 33 AF XY: 0.0000403 AC XY: 3AN XY: 74518
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.121C>T (p.R41W) alteration is located in exon 1 (coding exon 1) of the NEU2 gene. This alteration results from a C to T substitution at nucleotide position 121, causing the arginine (R) at amino acid position 41 to be replaced by a tryptophan (W). 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