chr5-140808495-G-C
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_018907.4(PCDHA4):āc.1308G>Cā(p.Trp436Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000471 in 1,614,062 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 (ā ).
Frequency
Consequence
NM_018907.4 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 |
---|---|---|---|---|---|---|---|
PCDHA4 | NM_018907.4 | c.1308G>C | p.Trp436Cys | missense_variant | 1/4 | ENST00000530339.2 | |
PCDHA1 | NM_018900.4 | c.2394+19811G>C | intron_variant | ENST00000504120.4 | |||
PCDHA2 | NM_018905.3 | c.2388+11143G>C | intron_variant | ENST00000526136.2 | |||
PCDHA3 | NM_018906.3 | c.2394+4904G>C | intron_variant | ENST00000522353.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PCDHA4 | ENST00000530339.2 | c.1308G>C | p.Trp436Cys | missense_variant | 1/4 | 1 | NM_018907.4 | P1 | |
PCDHA1 | ENST00000504120.4 | c.2394+19811G>C | intron_variant | 1 | NM_018900.4 | P1 | |||
PCDHA3 | ENST00000522353.3 | c.2394+4904G>C | intron_variant | 1 | NM_018906.3 | P1 | |||
PCDHA2 | ENST00000526136.2 | c.2388+11143G>C | intron_variant | 1 | NM_018905.3 | P1 | |||
ENST00000655235.1 | n.657+19398C>G | intron_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomes AF: 0.000158 AC: 24AN: 152250Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000756 AC: 19AN: 251460Hom.: 0 AF XY: 0.0000809 AC XY: 11AN XY: 135920
GnomAD4 exome AF: 0.0000356 AC: 52AN: 1461812Hom.: 0 Cov.: 35 AF XY: 0.0000289 AC XY: 21AN XY: 727202
GnomAD4 genome AF: 0.000158 AC: 24AN: 152250Hom.: 0 Cov.: 33 AF XY: 0.000134 AC XY: 10AN XY: 74388
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Apr 26, 2023 | The c.1308G>C (p.W436C) alteration is located in exon 1 (coding exon 1) of the PCDHA4 gene. This alteration results from a G to C substitution at nucleotide position 1308, causing the tryptophan (W) at amino acid position 436 to be replaced by a cysteine (C). 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