5-140786637-T-C
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_018900.4(PCDHA1):āc.347T>Cā(p.Val116Ala) variant causes a missense change. The variant allele was found at a frequency of 0.000141 in 1,614,160 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_018900.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PCDHA1 | NM_018900.4 | c.347T>C | p.Val116Ala | missense_variant | Exon 1 of 4 | ENST00000504120.4 | NP_061723.1 | |
PCDHA1 | NM_031410.2 | c.347T>C | p.Val116Ala | missense_variant | Exon 1 of 1 | NP_113598.1 | ||
PCDHA1 | NM_031411.3 | c.347T>C | p.Val116Ala | missense_variant | Exon 1 of 4 | NP_113599.1 | ||
PCDHA@ | n.140786637T>C | intragenic_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PCDHA1 | ENST00000504120.4 | c.347T>C | p.Val116Ala | missense_variant | Exon 1 of 4 | 1 | NM_018900.4 | ENSP00000420840.3 | ||
PCDHA1 | ENST00000394633.7 | c.347T>C | p.Val116Ala | missense_variant | Exon 1 of 4 | 1 | ENSP00000378129.3 | |||
PCDHA1 | ENST00000378133.4 | c.347T>C | p.Val116Ala | missense_variant | Exon 1 of 1 | 6 | ENSP00000367373.3 | |||
ENSG00000279726 | ENST00000655235.1 | n.2875A>G | non_coding_transcript_exon_variant | Exon 2 of 2 |
Frequencies
GnomAD3 genomes AF: 0.000105 AC: 16AN: 152158Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000716 AC: 18AN: 251474Hom.: 0 AF XY: 0.0000662 AC XY: 9AN XY: 135912
GnomAD4 exome AF: 0.000144 AC: 211AN: 1461884Hom.: 0 Cov.: 32 AF XY: 0.000129 AC XY: 94AN XY: 727242
GnomAD4 genome AF: 0.000105 AC: 16AN: 152276Hom.: 0 Cov.: 33 AF XY: 0.0000940 AC XY: 7AN XY: 74464
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.347T>C (p.V116A) alteration is located in exon 1 (coding exon 1) of the PCDHA1 gene. This alteration results from a T to C substitution at nucleotide position 347, causing the valine (V) at amino acid position 116 to be replaced by an alanine (A). 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