chr15-73556342-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_001042367.2(REC114):c.587C>T(p.Ala196Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000122 in 1,613,692 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/22 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001042367.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
REC114 | NM_001042367.2 | c.587C>T | p.Ala196Val | missense_variant | 5/6 | ENST00000331090.11 | |
REC114 | NM_001348772.2 | c.503C>T | p.Ala168Val | missense_variant | 4/5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
REC114 | ENST00000331090.11 | c.587C>T | p.Ala196Val | missense_variant | 5/6 | 1 | NM_001042367.2 | P1 | |
REC114 | ENST00000560581.1 | c.503C>T | p.Ala168Val | missense_variant | 4/5 | 2 |
Frequencies
GnomAD3 genomes AF: 0.0000526 AC: 8AN: 152160Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000765 AC: 19AN: 248520Hom.: 0 AF XY: 0.0000519 AC XY: 7AN XY: 134782
GnomAD4 exome AF: 0.000129 AC: 189AN: 1461414Hom.: 0 Cov.: 30 AF XY: 0.000117 AC XY: 85AN XY: 726978
GnomAD4 genome AF: 0.0000525 AC: 8AN: 152278Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74460
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jun 05, 2024 | The c.587C>T (p.A196V) alteration is located in exon 5 (coding exon 5) of the REC114 gene. This alteration results from a C to T substitution at nucleotide position 587, causing the alanine (A) at amino acid position 196 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