chr5-141122761-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.763C>T(p.Pro255Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.173 in 1,613,220 control chromosomes in the GnomAD database, including 25,125 homozygotes. 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 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. P255L) 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.763C>T | p.Pro255Ser | missense_variant | 1/1 | ENST00000194152.4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PCDHB4 | ENST00000194152.4 | c.763C>T | p.Pro255Ser | missense_variant | 1/1 | NM_018938.4 | P1 | ||
ENST00000624802.1 | n.365-22006G>A | intron_variant, non_coding_transcript_variant | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.177 AC: 26879AN: 151932Hom.: 2481 Cov.: 32
GnomAD3 exomes AF: 0.164 AC: 41212AN: 251376Hom.: 3629 AF XY: 0.162 AC XY: 21995AN XY: 135862
GnomAD4 exome AF: 0.172 AC: 251581AN: 1461172Hom.: 22643 Cov.: 36 AF XY: 0.171 AC XY: 123963AN XY: 726926
GnomAD4 genome ? AF: 0.177 AC: 26885AN: 152048Hom.: 2482 Cov.: 32 AF XY: 0.174 AC XY: 12925AN XY: 74352
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