chr5-140786341-G-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_018900.4(PCDHA1):c.51G>T(p.Trp17Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000204 in 1,613,702 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_018900.4 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 |
---|---|---|---|---|---|---|---|
PCDHA1 | NM_018900.4 | c.51G>T | p.Trp17Cys | missense_variant | 1/4 | ENST00000504120.4 | |
PCDHA1 | NM_031410.2 | c.51G>T | p.Trp17Cys | missense_variant | 1/1 | ||
PCDHA1 | NM_031411.3 | c.51G>T | p.Trp17Cys | missense_variant | 1/4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PCDHA1 | ENST00000504120.4 | c.51G>T | p.Trp17Cys | missense_variant | 1/4 | 1 | NM_018900.4 | P1 | |
PCDHA1 | ENST00000394633.7 | c.51G>T | p.Trp17Cys | missense_variant | 1/4 | 1 | |||
ENST00000655235.1 | n.3171C>A | non_coding_transcript_exon_variant | 2/2 | ||||||
PCDHA1 | ENST00000378133.4 | c.51G>T | p.Trp17Cys | missense_variant | 1/1 |
Frequencies
GnomAD3 genomes ? AF: 0.000145 AC: 22AN: 152232Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000279 AC: 7AN: 250728Hom.: 1 AF XY: 0.0000147 AC XY: 2AN XY: 135624
GnomAD4 exome AF: 0.00000753 AC: 11AN: 1461352Hom.: 1 Cov.: 32 AF XY: 0.00000275 AC XY: 2AN XY: 726936
GnomAD4 genome ? AF: 0.000144 AC: 22AN: 152350Hom.: 0 Cov.: 33 AF XY: 0.000134 AC XY: 10AN XY: 74500
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Apr 11, 2023 | The c.51G>T (p.W17C) alteration is located in exon 1 (coding exon 1) of the PCDHA1 gene. This alteration results from a G to T substitution at nucleotide position 51, causing the tryptophan (W) at amino acid position 17 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