chr5-140808691-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_018907.4(PCDHA4):c.1504C>T(p.Arg502Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000819 in 1,611,952 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 11/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_018907.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PCDHA4 | NM_018907.4 | c.1504C>T | p.Arg502Cys | missense_variant | 1/4 | ENST00000530339.2 | |
PCDHA1 | NM_018900.4 | c.2394+20007C>T | intron_variant | ENST00000504120.4 | |||
PCDHA2 | NM_018905.3 | c.2388+11339C>T | intron_variant | ENST00000526136.2 | |||
PCDHA3 | NM_018906.3 | c.2394+5100C>T | intron_variant | ENST00000522353.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PCDHA4 | ENST00000530339.2 | c.1504C>T | p.Arg502Cys | missense_variant | 1/4 | 1 | NM_018907.4 | P1 | |
PCDHA1 | ENST00000504120.4 | c.2394+20007C>T | intron_variant | 1 | NM_018900.4 | P1 | |||
PCDHA3 | ENST00000522353.3 | c.2394+5100C>T | intron_variant | 1 | NM_018906.3 | P1 | |||
PCDHA2 | ENST00000526136.2 | c.2388+11339C>T | intron_variant | 1 | NM_018905.3 | P1 | |||
ENST00000655235.1 | n.657+19202G>A | intron_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomes ? AF: 0.000237 AC: 36AN: 152102Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000679 AC: 17AN: 250496Hom.: 0 AF XY: 0.0000590 AC XY: 8AN XY: 135518
GnomAD4 exome AF: 0.0000658 AC: 96AN: 1459850Hom.: 0 Cov.: 36 AF XY: 0.0000675 AC XY: 49AN XY: 726270
GnomAD4 genome ? AF: 0.000237 AC: 36AN: 152102Hom.: 0 Cov.: 33 AF XY: 0.000242 AC XY: 18AN XY: 74282
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Feb 13, 2023 | The c.1504C>T (p.R502C) alteration is located in exon 1 (coding exon 1) of the PCDHA4 gene. This alteration results from a C to T substitution at nucleotide position 1504, causing the arginine (R) at amino acid position 502 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