chr14-57232709-T-A
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 1P and 0B. PP3
The NM_006544.4(EXOC5):c.896A>T(p.Asp299Val) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000771 in 1,555,920 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. D299N) has been classified as Uncertain significance.
Frequency
Consequence
NM_006544.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
EXOC5 | NM_006544.4 | c.896A>T | p.Asp299Val | missense_variant | 10/18 | ENST00000621441.5 | |
EXOC5 | XM_005267272.4 | c.1010A>T | p.Asp337Val | missense_variant | 10/18 | ||
EXOC5 | XM_047430882.1 | c.731A>T | p.Asp244Val | missense_variant | 10/18 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
EXOC5 | ENST00000621441.5 | c.896A>T | p.Asp299Val | missense_variant | 10/18 | 1 | NM_006544.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000197 AC: 3AN: 152186Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000430 AC: 1AN: 232530Hom.: 0 AF XY: 0.00000792 AC XY: 1AN XY: 126236
GnomAD4 exome AF: 0.00000641 AC: 9AN: 1403734Hom.: 0 Cov.: 22 AF XY: 0.00000714 AC XY: 5AN XY: 700142
GnomAD4 genome ? AF: 0.0000197 AC: 3AN: 152186Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74368
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 28, 2022 | The c.896A>T (p.D299V) alteration is located in exon 10 (coding exon 10) of the EXOC5 gene. This alteration results from a A to T substitution at nucleotide position 896, causing the aspartic acid (D) at amino acid position 299 to be replaced by a valine (V). 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