5-140795974-C-A
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_018905.3(PCDHA2):c.1010C>A(p.Ser337Ter) variant causes a stop gained change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000684 in 1,461,846 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 (no stars). Variant results in nonsense mediated mRNA decay.
Frequency
Consequence
NM_018905.3 stop_gained
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/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PCDHA2 | NM_018905.3 | c.1010C>A | p.Ser337Ter | stop_gained | 1/4 | ENST00000526136.2 | |
PCDHA1 | NM_018900.4 | c.2394+7290C>A | intron_variant | ENST00000504120.4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PCDHA2 | ENST00000526136.2 | c.1010C>A | p.Ser337Ter | stop_gained | 1/4 | 1 | NM_018905.3 | P1 | |
PCDHA1 | ENST00000504120.4 | c.2394+7290C>A | intron_variant | 1 | NM_018900.4 | P1 | |||
ENST00000655235.1 | n.658-7120G>T | intron_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD4 exome AF: 6.84e-7 AC: 1AN: 1461846Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 727224
GnomAD4 genome Cov.: 33
ClinVar
Submissions by phenotype
not provided Uncertain:1
Uncertain significance, no assertion criteria provided | literature only | Richard Lifton Laboratory, Yale University School of Medicine | - | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at