22-41572093-G-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_014460.4(CSDC2):c.128G>A(p.Arg43Gln) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.000053 in 1,358,340 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_014460.4 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: 0.000118 AC: 18AN: 151924Hom.: 1 Cov.: 32
GnomAD3 exomes AF: 0.0000633 AC: 5AN: 79008Hom.: 0 AF XY: 0.0000485 AC XY: 2AN XY: 41212
GnomAD4 exome AF: 0.0000448 AC: 54AN: 1206298Hom.: 0 Cov.: 32 AF XY: 0.0000447 AC XY: 26AN XY: 581612
GnomAD4 genome AF: 0.000118 AC: 18AN: 152042Hom.: 1 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74318
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.128G>A (p.R43Q) alteration is located in exon 2 (coding exon 1) of the CSDC2 gene. This alteration results from a G to A substitution at nucleotide position 128, causing the arginine (R) at amino acid position 43 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