14-57209596-C-T
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BS2
The NM_006544.4(EXOC5):c.1909G>A(p.Glu637Lys) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000347 in 1,612,420 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_006544.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
EXOC5 | NM_006544.4 | c.1909G>A | p.Glu637Lys | missense_variant | Exon 17 of 18 | ENST00000621441.5 | NP_006535.1 | |
EXOC5 | XM_005267272.4 | c.2023G>A | p.Glu675Lys | missense_variant | Exon 17 of 18 | XP_005267329.1 | ||
EXOC5 | XM_047430882.1 | c.1744G>A | p.Glu582Lys | missense_variant | Exon 17 of 18 | XP_047286838.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000263 AC: 4AN: 152064Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000165 AC: 41AN: 248018Hom.: 0 AF XY: 0.000134 AC XY: 18AN XY: 134532
GnomAD4 exome AF: 0.0000356 AC: 52AN: 1460356Hom.: 0 Cov.: 30 AF XY: 0.0000317 AC XY: 23AN XY: 726496
GnomAD4 genome AF: 0.0000263 AC: 4AN: 152064Hom.: 0 Cov.: 32 AF XY: 0.0000404 AC XY: 3AN XY: 74272
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.1909G>A (p.E637K) alteration is located in exon 17 (coding exon 17) of the EXOC5 gene. This alteration results from a G to A substitution at nucleotide position 1909, causing the glutamic acid (E) at amino acid position 637 to be replaced by a lysine (K). 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