chr1-2479914-G-T
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_014638.4(PLCH2):c.452G>T(p.Arg151Leu) variant causes a missense change. The variant allele was found at a frequency of 0.0000155 in 1,610,956 control chromosomes in the GnomAD database, with no homozygous occurrence. 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. R151C) has been classified as Uncertain significance.
Frequency
Consequence
NM_014638.4 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 |
---|---|---|---|---|---|---|---|
PLCH2 | NM_014638.4 | c.452G>T | p.Arg151Leu | missense_variant | 3/22 | ENST00000378486.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PLCH2 | ENST00000378486.8 | c.452G>T | p.Arg151Leu | missense_variant | 3/22 | 1 | NM_014638.4 | P2 |
Frequencies
GnomAD3 genomes AF: 0.0000263 AC: 4AN: 152190Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000922 AC: 22AN: 238638Hom.: 0 AF XY: 0.0000990 AC XY: 13AN XY: 131328
GnomAD4 exome AF: 0.0000144 AC: 21AN: 1458766Hom.: 0 Cov.: 30 AF XY: 0.0000165 AC XY: 12AN XY: 725534
GnomAD4 genome AF: 0.0000263 AC: 4AN: 152190Hom.: 0 Cov.: 32 AF XY: 0.0000538 AC XY: 4AN XY: 74356
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Nov 18, 2022 | The c.452G>T (p.R151L) alteration is located in exon 3 (coding exon 3) of the PLCH2 gene. This alteration results from a G to T substitution at nucleotide position 452, causing the arginine (R) at amino acid position 151 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