5-446269-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_007277.5(EXOC3):c.64C>T(p.Arg22Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000223 in 1,613,836 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_007277.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
EXOC3 | NM_007277.5 | c.64C>T | p.Arg22Cys | missense_variant | Exon 2 of 13 | ENST00000512944.6 | NP_009208.2 | |
EXOC3 | XM_047416683.1 | c.64C>T | p.Arg22Cys | missense_variant | Exon 2 of 7 | XP_047272639.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000184 AC: 28AN: 152200Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000454 AC: 113AN: 249138Hom.: 0 AF XY: 0.000437 AC XY: 59AN XY: 135156
GnomAD4 exome AF: 0.000227 AC: 332AN: 1461636Hom.: 1 Cov.: 31 AF XY: 0.000250 AC XY: 182AN XY: 727100
GnomAD4 genome AF: 0.000184 AC: 28AN: 152200Hom.: 0 Cov.: 33 AF XY: 0.000215 AC XY: 16AN XY: 74352
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.64C>T (p.R22C) alteration is located in exon 2 (coding exon 1) of the EXOC3 gene. This alteration results from a C to T substitution at nucleotide position 64, causing the arginine (R) at amino acid position 22 to be replaced by a cysteine (C). 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