chr5-141122762-C-T
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_018938.4(PCDHB4):c.764C>T(p.Pro255Leu) variant causes a missense change. The variant allele was found at a frequency of 0.173 in 1,613,194 control chromosomes in the GnomAD database, including 25,127 homozygotes. 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 Benign (★). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. P255S) has been classified as Benign.
Frequency
Consequence
NM_018938.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PCDHB4 | NM_018938.4 | c.764C>T | p.Pro255Leu | missense_variant | 1/1 | ENST00000194152.4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PCDHB4 | ENST00000194152.4 | c.764C>T | p.Pro255Leu | missense_variant | 1/1 | NM_018938.4 | P1 | ||
ENST00000624802.1 | n.365-22007G>A | intron_variant, non_coding_transcript_variant | 3 |
Frequencies
GnomAD3 genomes AF: 0.177 AC: 26884AN: 151904Hom.: 2482 Cov.: 32
GnomAD3 exomes AF: 0.164 AC: 41211AN: 251378Hom.: 3629 AF XY: 0.162 AC XY: 21993AN XY: 135862
GnomAD4 exome AF: 0.172 AC: 251579AN: 1461174Hom.: 22644 Cov.: 36 AF XY: 0.171 AC XY: 123957AN XY: 726914
GnomAD4 genome AF: 0.177 AC: 26890AN: 152020Hom.: 2483 Cov.: 32 AF XY: 0.174 AC XY: 12930AN XY: 74322
ClinVar
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Oct 12, 2018 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at