chr14-103102612-G-A
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_001077594.2(EXOC3L4):c.889G>A(p.Val297Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00511 in 1,499,942 control chromosomes in the GnomAD database, including 352 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Consequence
NM_001077594.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
EXOC3L4 | NM_001077594.2 | c.889G>A | p.Val297Met | missense_variant | 3/12 | ENST00000688303.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
EXOC3L4 | ENST00000688303.1 | c.889G>A | p.Val297Met | missense_variant | 3/12 | NM_001077594.2 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0271 AC: 4121AN: 152212Hom.: 189 Cov.: 34
GnomAD3 exomes AF: 0.00353 AC: 351AN: 99326Hom.: 8 AF XY: 0.00276 AC XY: 153AN XY: 55368
GnomAD4 exome AF: 0.00262 AC: 3535AN: 1347614Hom.: 162 Cov.: 36 AF XY: 0.00221 AC XY: 1468AN XY: 664038
GnomAD4 genome ? AF: 0.0271 AC: 4124AN: 152328Hom.: 190 Cov.: 34 AF XY: 0.0261 AC XY: 1941AN XY: 74496
ClinVar
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Oct 16, 2019 | This variant is associated with the following publications: (PMID: 30255815) - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at