5-140822890-G-C
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_ModerateBP6_Moderate
The NM_018908.3(PCDHA5):āc.1115G>Cā(p.Ser372Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000279 in 1,614,098 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (ā ).
Frequency
Consequence
NM_018908.3 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 |
---|---|---|---|---|---|---|---|---|
PCDHA5 | NM_018908.3 | c.1115G>C | p.Ser372Thr | missense_variant | 1/4 | ENST00000529859.2 | NP_061731.1 | |
PCDHA1 | NM_018900.4 | c.2394+34206G>C | intron_variant | ENST00000504120.4 | NP_061723.1 | |||
PCDHA2 | NM_018905.3 | c.2388+25538G>C | intron_variant | ENST00000526136.2 | NP_061728.1 | |||
PCDHA3 | NM_018906.3 | c.2394+19299G>C | intron_variant | ENST00000522353.3 | NP_061729.1 | |||
PCDHA4 | NM_018907.4 | c.2385+13318G>C | intron_variant | ENST00000530339.2 | NP_061730.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PCDHA5 | ENST00000529859.2 | c.1115G>C | p.Ser372Thr | missense_variant | 1/4 | 1 | NM_018908.3 | ENSP00000436557 | P1 | |
PCDHA1 | ENST00000504120.4 | c.2394+34206G>C | intron_variant | 1 | NM_018900.4 | ENSP00000420840 | P1 | |||
PCDHA3 | ENST00000522353.3 | c.2394+19299G>C | intron_variant | 1 | NM_018906.3 | ENSP00000429808 | P1 | |||
PCDHA2 | ENST00000526136.2 | c.2388+25538G>C | intron_variant | 1 | NM_018905.3 | ENSP00000431748 | P1 | |||
PCDHA4 | ENST00000530339.2 | c.2385+13318G>C | intron_variant | 1 | NM_018907.4 | ENSP00000435300 | P1 | |||
ENST00000655235.1 | n.657+5003C>G | intron_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152228Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.00000398 AC: 1AN: 251474Hom.: 0 AF XY: 0.00000736 AC XY: 1AN XY: 135916
GnomAD4 exome AF: 0.0000301 AC: 44AN: 1461870Hom.: 0 Cov.: 34 AF XY: 0.0000330 AC XY: 24AN XY: 727236
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152228Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 74380
ClinVar
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Sep 14, 2022 | This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at