5-141351203-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_018922.3(PCDHGB1):c.943G>A(p.Val315Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000545 in 1,613,946 control chromosomes in the GnomAD database, including 1 homozygotes. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_018922.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PCDHGB1 | NM_018922.3 | c.943G>A | p.Val315Met | missense_variant | Exon 1 of 4 | ENST00000523390.2 | NP_061745.1 | |
PCDHGA2 | NM_018915.4 | c.2424+9808G>A | intron_variant | Intron 1 of 3 | ENST00000394576.3 | NP_061738.1 | ||
PCDHGA3 | NM_018916.4 | c.2424+4746G>A | intron_variant | Intron 1 of 3 | ENST00000253812.8 | NP_061739.2 | ||
PCDHGA1 | NM_018912.3 | c.2421+18098G>A | intron_variant | Intron 1 of 3 | ENST00000517417.3 | NP_061735.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PCDHGB1 | ENST00000523390.2 | c.943G>A | p.Val315Met | missense_variant | Exon 1 of 4 | 1 | NM_018922.3 | ENSP00000429273.1 | ||
PCDHGA3 | ENST00000253812.8 | c.2424+4746G>A | intron_variant | Intron 1 of 3 | 1 | NM_018916.4 | ENSP00000253812.7 | |||
PCDHGA2 | ENST00000394576.3 | c.2424+9808G>A | intron_variant | Intron 1 of 3 | 1 | NM_018915.4 | ENSP00000378077.2 | |||
PCDHGA1 | ENST00000517417.3 | c.2421+18098G>A | intron_variant | Intron 1 of 3 | 1 | NM_018912.3 | ENSP00000431083.1 |
Frequencies
GnomAD3 genomes AF: 0.0000197 AC: 3AN: 152250Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000401 AC: 10AN: 249224Hom.: 0 AF XY: 0.0000370 AC XY: 5AN XY: 135204
GnomAD4 exome AF: 0.0000582 AC: 85AN: 1461696Hom.: 1 Cov.: 33 AF XY: 0.0000605 AC XY: 44AN XY: 727132
GnomAD4 genome AF: 0.0000197 AC: 3AN: 152250Hom.: 0 Cov.: 33 AF XY: 0.0000269 AC XY: 2AN XY: 74384
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.943G>A (p.V315M) alteration is located in exon 1 (coding exon 1) of the PCDHGB1 gene. This alteration results from a G to A substitution at nucleotide position 943, causing the valine (V) at amino acid position 315 to be replaced by a methionine (M). 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