chr5-141351467-G-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_018922.3(PCDHGB1):c.1207G>T(p.Ala403Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000062 in 1,613,546 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 (★).
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 | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PCDHGB1 | NM_018922.3 | c.1207G>T | p.Ala403Ser | missense_variant | 1/4 | ENST00000523390.2 | NP_061745.1 | |
PCDHGA1 | NM_018912.3 | c.2421+18362G>T | intron_variant | ENST00000517417.3 | NP_061735.1 | |||
PCDHGA2 | NM_018915.4 | c.2424+10072G>T | intron_variant | ENST00000394576.3 | NP_061738.1 | |||
PCDHGA3 | NM_018916.4 | c.2424+5010G>T | intron_variant | ENST00000253812.8 | NP_061739.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PCDHGB1 | ENST00000523390.2 | c.1207G>T | p.Ala403Ser | missense_variant | 1/4 | 1 | NM_018922.3 | ENSP00000429273 | P1 | |
PCDHGA3 | ENST00000253812.8 | c.2424+5010G>T | intron_variant | 1 | NM_018916.4 | ENSP00000253812 | P1 | |||
PCDHGA2 | ENST00000394576.3 | c.2424+10072G>T | intron_variant | 1 | NM_018915.4 | ENSP00000378077 | P1 | |||
PCDHGA1 | ENST00000517417.3 | c.2421+18362G>T | intron_variant | 1 | NM_018912.3 | ENSP00000431083 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000131 AC: 2AN: 152226Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000322 AC: 8AN: 248310Hom.: 0 AF XY: 0.0000297 AC XY: 4AN XY: 134726
GnomAD4 exome AF: 0.00000547 AC: 8AN: 1461320Hom.: 0 Cov.: 33 AF XY: 0.00000413 AC XY: 3AN XY: 726904
GnomAD4 genome AF: 0.0000131 AC: 2AN: 152226Hom.: 0 Cov.: 33 AF XY: 0.0000134 AC XY: 1AN XY: 74376
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 29, 2024 | The c.1207G>T (p.A403S) alteration is located in exon 1 (coding exon 1) of the PCDHGB1 gene. This alteration results from a G to T substitution at nucleotide position 1207, causing the alanine (A) at amino acid position 403 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