5-141344911-A-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_018916.4(PCDHGA3):c.878A>T(p.His293Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000186 in 1,613,804 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_018916.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PCDHGA3 | NM_018916.4 | c.878A>T | p.His293Leu | missense_variant | 1/4 | ENST00000253812.8 | NP_061739.2 | |
PCDHGA1 | NM_018912.3 | c.2421+11806A>T | intron_variant | ENST00000517417.3 | NP_061735.1 | |||
PCDHGA2 | NM_018915.4 | c.2424+3516A>T | intron_variant | ENST00000394576.3 | NP_061738.1 | |||
PCDHGA3 | NM_032011.2 | c.878A>T | p.His293Leu | missense_variant | 1/1 | NP_114400.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PCDHGA3 | ENST00000253812.8 | c.878A>T | p.His293Leu | missense_variant | 1/4 | 1 | NM_018916.4 | ENSP00000253812 | P1 | |
PCDHGA2 | ENST00000394576.3 | c.2424+3516A>T | intron_variant | 1 | NM_018915.4 | ENSP00000378077 | P1 | |||
PCDHGA1 | ENST00000517417.3 | c.2421+11806A>T | intron_variant | 1 | NM_018912.3 | ENSP00000431083 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000131 AC: 2AN: 152196Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000402 AC: 1AN: 248956Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 135126
GnomAD4 exome AF: 6.84e-7 AC: 1AN: 1461608Hom.: 0 Cov.: 34 AF XY: 0.00 AC XY: 0AN XY: 727094
GnomAD4 genome AF: 0.0000131 AC: 2AN: 152196Hom.: 0 Cov.: 32 AF XY: 0.0000134 AC XY: 1AN XY: 74356
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Feb 15, 2023 | The c.878A>T (p.H293L) alteration is located in exon 1 (coding exon 1) of the PCDHGA3 gene. This alteration results from a A to T substitution at nucleotide position 878, causing the histidine (H) at amino acid position 293 to be replaced by a leucine (L). 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