5-141854248-C-T
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 2P and 5B. PM2BP4BS2
The NM_032420.5(PCDH1):c.3508G>A(p.Gly1170Ser) variant causes a missense change. The variant allele was found at a frequency of 0.00000343 in 1,459,336 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_032420.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PCDH1 | NM_032420.5 | c.3508G>A | p.Gly1170Ser | missense_variant | Exon 5 of 5 | ENST00000287008.8 | NP_115796.2 | |
PCDH1 | XM_005268452.4 | c.3556G>A | p.Gly1186Ser | missense_variant | Exon 5 of 5 | XP_005268509.2 | ||
PCDH1 | XM_017009517.3 | c.2371G>A | p.Gly791Ser | missense_variant | Exon 4 of 4 | XP_016865006.1 | ||
PCDH1 | XM_005268454.6 | c.*202G>A | 3_prime_UTR_variant | Exon 6 of 6 | XP_005268511.2 |
Ensembl
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 exomes AF: 0.0000125 AC: 3AN: 240554Hom.: 0 AF XY: 0.00000761 AC XY: 1AN XY: 131326
GnomAD4 exome AF: 0.00000343 AC: 5AN: 1459336Hom.: 0 Cov.: 31 AF XY: 0.00000276 AC XY: 2AN XY: 725826
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.3508G>A (p.G1170S) alteration is located in exon 5 (coding exon 5) of the PCDH1 gene. This alteration results from a G to A substitution at nucleotide position 3508, causing the glycine (G) at amino acid position 1170 to be replaced by a serine (S). 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