5-141350958-A-G
Variant summary
Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PM2PP3_Moderate
The NM_018922.3(PCDHGB1):āc.698A>Gā(p.Asn233Ser) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000558 in 1,613,978 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_018922.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PCDHGB1 | NM_018922.3 | c.698A>G | p.Asn233Ser | missense_variant | Exon 1 of 4 | ENST00000523390.2 | NP_061745.1 | |
PCDHGA2 | NM_018915.4 | c.2424+9563A>G | intron_variant | Intron 1 of 3 | ENST00000394576.3 | NP_061738.1 | ||
PCDHGA3 | NM_018916.4 | c.2424+4501A>G | intron_variant | Intron 1 of 3 | ENST00000253812.8 | NP_061739.2 | ||
PCDHGA1 | NM_018912.3 | c.2421+17853A>G | 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.698A>G | p.Asn233Ser | missense_variant | Exon 1 of 4 | 1 | NM_018922.3 | ENSP00000429273.1 | ||
PCDHGA3 | ENST00000253812.8 | c.2424+4501A>G | intron_variant | Intron 1 of 3 | 1 | NM_018916.4 | ENSP00000253812.7 | |||
PCDHGA2 | ENST00000394576.3 | c.2424+9563A>G | intron_variant | Intron 1 of 3 | 1 | NM_018915.4 | ENSP00000378077.2 | |||
PCDHGA1 | ENST00000517417.3 | c.2421+17853A>G | intron_variant | Intron 1 of 3 | 1 | NM_018912.3 | ENSP00000431083.1 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152270Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000160 AC: 4AN: 249244Hom.: 0 AF XY: 0.0000296 AC XY: 4AN XY: 135226
GnomAD4 exome AF: 0.00000547 AC: 8AN: 1461708Hom.: 0 Cov.: 33 AF XY: 0.00000825 AC XY: 6AN XY: 727136
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152270Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 74394
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.698A>G (p.N233S) alteration is located in exon 1 (coding exon 1) of the PCDHGB1 gene. This alteration results from a A to G substitution at nucleotide position 698, causing the asparagine (N) at amino acid position 233 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