21-41899151-G-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_015500.2(C2CD2):c.1772C>A(p.Ala591Glu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000254 in 1,613,354 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_015500.2 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: 0.0000329 AC: 5AN: 152138Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000240 AC: 6AN: 250176Hom.: 0 AF XY: 0.0000222 AC XY: 3AN XY: 135380
GnomAD4 exome AF: 0.0000246 AC: 36AN: 1461216Hom.: 0 Cov.: 33 AF XY: 0.0000303 AC XY: 22AN XY: 726968
GnomAD4 genome AF: 0.0000329 AC: 5AN: 152138Hom.: 0 Cov.: 32 AF XY: 0.0000404 AC XY: 3AN XY: 74314
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.1772C>A (p.A591E) alteration is located in exon 13 (coding exon 13) of the C2CD2 gene. This alteration results from a C to A substitution at nucleotide position 1772, causing the alanine (A) at amino acid position 591 to be replaced by a glutamic acid (E). 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