chr5-141351445-G-C
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_018922.3(PCDHGB1):āc.1185G>Cā(p.Lys395Asn) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000157 in 1,460,602 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/20 in silico tools predict a benign 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 Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PCDHGB1 | NM_018922.3 | c.1185G>C | p.Lys395Asn | missense_variant | 1/4 | ENST00000523390.2 | |
PCDHGA1 | NM_018912.3 | c.2421+18340G>C | intron_variant | ENST00000517417.3 | |||
PCDHGA2 | NM_018915.4 | c.2424+10050G>C | intron_variant | ENST00000394576.3 | |||
PCDHGA3 | NM_018916.4 | c.2424+4988G>C | intron_variant | ENST00000253812.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PCDHGB1 | ENST00000523390.2 | c.1185G>C | p.Lys395Asn | missense_variant | 1/4 | 1 | NM_018922.3 | P1 | |
PCDHGA3 | ENST00000253812.8 | c.2424+4988G>C | intron_variant | 1 | NM_018916.4 | P1 | |||
PCDHGA2 | ENST00000394576.3 | c.2424+10050G>C | intron_variant | 1 | NM_018915.4 | P1 | |||
PCDHGA1 | ENST00000517417.3 | c.2421+18340G>C | intron_variant | 1 | NM_018912.3 | P1 |
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD3 exomes AF: 0.0000203 AC: 5AN: 246356Hom.: 0 AF XY: 0.0000224 AC XY: 3AN XY: 133692
GnomAD4 exome AF: 0.0000157 AC: 23AN: 1460602Hom.: 0 Cov.: 33 AF XY: 0.0000206 AC XY: 15AN XY: 726486
GnomAD4 genome Cov.: 33
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | May 30, 2024 | The c.1185G>C (p.K395N) alteration is located in exon 1 (coding exon 1) of the PCDHGB1 gene. This alteration results from a G to C substitution at nucleotide position 1185, causing the lysine (K) at amino acid position 395 to be replaced by an asparagine (N). 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