5-140802045-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_018906.3(PCDHA3):c.848C>T(p.Thr283Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000124 in 1,614,022 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_018906.3 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 |
---|---|---|---|---|---|---|---|
PCDHA3 | NM_018906.3 | c.848C>T | p.Thr283Met | missense_variant | 1/4 | ENST00000522353.3 | |
PCDHA1 | NM_018900.4 | c.2394+13361C>T | intron_variant | ENST00000504120.4 | |||
PCDHA2 | NM_018905.3 | c.2388+4693C>T | intron_variant | ENST00000526136.2 | |||
LOC124901089 | XR_007058969.1 | n.2277G>A | non_coding_transcript_exon_variant | 2/3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PCDHA3 | ENST00000522353.3 | c.848C>T | p.Thr283Met | missense_variant | 1/4 | 1 | NM_018906.3 | P1 | |
PCDHA1 | ENST00000504120.4 | c.2394+13361C>T | intron_variant | 1 | NM_018900.4 | P1 | |||
PCDHA2 | ENST00000526136.2 | c.2388+4693C>T | intron_variant | 1 | NM_018905.3 | P1 | |||
ENST00000655235.1 | n.658-13191G>A | intron_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomes ? AF: 0.0000460 AC: 7AN: 152172Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000557 AC: 14AN: 251408Hom.: 0 AF XY: 0.0000221 AC XY: 3AN XY: 135886
GnomAD4 exome AF: 0.00000889 AC: 13AN: 1461850Hom.: 0 Cov.: 89 AF XY: 0.00000688 AC XY: 5AN XY: 727216
GnomAD4 genome ? AF: 0.0000460 AC: 7AN: 152172Hom.: 0 Cov.: 33 AF XY: 0.0000404 AC XY: 3AN XY: 74338
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Feb 28, 2023 | The c.848C>T (p.T283M) alteration is located in exon 1 (coding exon 1) of the PCDHA3 gene. This alteration results from a C to T substitution at nucleotide position 848, causing the threonine (T) at amino acid position 283 to be replaced by a methionine (M). 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