chr5-140808677-G-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_018907.4(PCDHA4):c.1490G>T(p.Arg497Leu) variant causes a missense change. The variant allele was found at a frequency of 0.000000685 in 1,460,276 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/19 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 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PCDHA4 | NM_018907.4 | c.1490G>T | p.Arg497Leu | missense_variant | 1/4 | ENST00000530339.2 | |
PCDHA1 | NM_018900.4 | c.2394+19993G>T | intron_variant | ENST00000504120.4 | |||
PCDHA2 | NM_018905.3 | c.2388+11325G>T | intron_variant | ENST00000526136.2 | |||
PCDHA3 | NM_018906.3 | c.2394+5086G>T | intron_variant | ENST00000522353.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PCDHA4 | ENST00000530339.2 | c.1490G>T | p.Arg497Leu | missense_variant | 1/4 | 1 | NM_018907.4 | P1 | |
PCDHA1 | ENST00000504120.4 | c.2394+19993G>T | intron_variant | 1 | NM_018900.4 | P1 | |||
PCDHA3 | ENST00000522353.3 | c.2394+5086G>T | intron_variant | 1 | NM_018906.3 | P1 | |||
PCDHA2 | ENST00000526136.2 | c.2388+11325G>T | intron_variant | 1 | NM_018905.3 | P1 | |||
ENST00000655235.1 | n.657+19216C>A | intron_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomes ? Cov.: 33
GnomAD4 exome AF: 6.85e-7 AC: 1AN: 1460276Hom.: 0 Cov.: 36 AF XY: 0.00 AC XY: 0AN XY: 726480
GnomAD4 genome ? Cov.: 33
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jul 12, 2023 | The c.1490G>T (p.R497L) alteration is located in exon 1 (coding exon 1) of the PCDHA4 gene. This alteration results from a G to T substitution at nucleotide position 1490, causing the arginine (R) at amino acid position 497 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
Publications
No publications associated with this variant yet.