15-73556335-G-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001042367.2(REC114):c.580G>T(p.Val194Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000787 in 1,613,822 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign 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. V194I) has been classified as Uncertain significance.
Frequency
Consequence
NM_001042367.2 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/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
REC114 | NM_001042367.2 | c.580G>T | p.Val194Leu | missense_variant | 5/6 | ENST00000331090.11 | |
REC114 | NM_001348772.2 | c.496G>T | p.Val166Leu | missense_variant | 4/5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
REC114 | ENST00000331090.11 | c.580G>T | p.Val194Leu | missense_variant | 5/6 | 1 | NM_001042367.2 | P1 | |
REC114 | ENST00000560581.1 | c.496G>T | p.Val166Leu | missense_variant | 4/5 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.000138 AC: 21AN: 152212Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000684 AC: 17AN: 248630Hom.: 0 AF XY: 0.0000742 AC XY: 10AN XY: 134826
GnomAD4 exome AF: 0.0000725 AC: 106AN: 1461492Hom.: 0 Cov.: 30 AF XY: 0.0000812 AC XY: 59AN XY: 727010
GnomAD4 genome ? AF: 0.000138 AC: 21AN: 152330Hom.: 0 Cov.: 32 AF XY: 0.000134 AC XY: 10AN XY: 74492
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jul 21, 2021 | The c.580G>T (p.V194L) alteration is located in exon 5 (coding exon 5) of the REC114 gene. This alteration results from a G to T substitution at nucleotide position 580, causing the valine (V) at amino acid position 194 to be replaced by a leucine (L). 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