chr1-2476632-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_014638.4(PLCH2):c.44C>T(p.Thr15Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000231 in 1,603,754 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar 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 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PLCH2 | NM_014638.4 | c.44C>T | p.Thr15Met | missense_variant | 1/22 | ENST00000378486.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PLCH2 | ENST00000378486.8 | c.44C>T | p.Thr15Met | missense_variant | 1/22 | 1 | NM_014638.4 | P2 | |
PLCH2 | ENST00000419816.6 | c.44C>T | p.Thr15Met | missense_variant | 1/22 | 5 | P2 | ||
PLCH2 | ENST00000449969.5 | c.44-1844C>T | intron_variant | 5 | A2 | ||||
PLCH2 | ENST00000609981.5 | c.116-1844C>T | intron_variant | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.0000197 AC: 3AN: 152214Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000647 AC: 15AN: 231832Hom.: 0 AF XY: 0.0000792 AC XY: 10AN XY: 126324
GnomAD4 exome AF: 0.0000234 AC: 34AN: 1451540Hom.: 0 Cov.: 31 AF XY: 0.0000305 AC XY: 22AN XY: 721394
GnomAD4 genome ? AF: 0.0000197 AC: 3AN: 152214Hom.: 0 Cov.: 33 AF XY: 0.0000403 AC XY: 3AN XY: 74354
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 21, 2022 | The c.44C>T (p.T15M) alteration is located in exon 1 (coding exon 1) of the PLCH2 gene. This alteration results from a C to T substitution at nucleotide position 44, causing the threonine (T) at amino acid position 15 to be replaced by a methionine (M). 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