5-141209229-G-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_018932.4(PCDHB12):c.322G>T(p.Val108Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000966 in 1,614,074 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_018932.4 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 | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PCDHB12 | NM_018932.4 | c.322G>T | p.Val108Leu | missense_variant | 1/1 | ENST00000239450.4 | NP_061755.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PCDHB12 | ENST00000239450.4 | c.322G>T | p.Val108Leu | missense_variant | 1/1 | NM_018932.4 | ENSP00000239450 | P1 | ||
ENST00000624192.1 | n.72+32444C>A | intron_variant, non_coding_transcript_variant | 5 | |||||||
PCDHB12 | ENST00000622978.1 | c.165+157G>T | intron_variant | 2 | ENSP00000485352 | |||||
PCDHB12 | ENST00000624949.1 | c.-99+287G>T | intron_variant | 2 | ENSP00000485303 |
Frequencies
GnomAD3 genomes AF: 0.0000789 AC: 12AN: 152180Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000358 AC: 9AN: 251068Hom.: 0 AF XY: 0.0000368 AC XY: 5AN XY: 135884
GnomAD4 exome AF: 0.0000985 AC: 144AN: 1461894Hom.: 1 Cov.: 31 AF XY: 0.000106 AC XY: 77AN XY: 727248
GnomAD4 genome AF: 0.0000789 AC: 12AN: 152180Hom.: 0 Cov.: 32 AF XY: 0.0000807 AC XY: 6AN XY: 74342
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | May 04, 2023 | The c.322G>T (p.V108L) alteration is located in exon 1 (coding exon 1) of the PCDHB12 gene. This alteration results from a G to T substitution at nucleotide position 322, causing the valine (V) at amino acid position 108 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