10-102403013-G-C
Variant names:
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_002779.5(PSD):c.*187C>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: not found (cov: 28)
Exomes 𝑓: 0.0 ( 0 hom. )
Failed GnomAD Quality Control
Consequence
PSD
NM_002779.5 3_prime_UTR
NM_002779.5 3_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.109
Genes affected
PSD (HGNC:9507): (pleckstrin and Sec7 domain containing) This gene encodes a Plekstrin homology and SEC7 domains-containing protein that functions as a guanine nucleotide exchange factor. The encoded protein regulates signal transduction by activating ADP-ribosylation factor 6. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Aug 2012]
Genome browser will be placed here
ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -2 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.83).
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PSD | NM_002779.5 | c.*187C>G | 3_prime_UTR_variant | Exon 17 of 17 | ENST00000020673.6 | NP_002770.3 | ||
PSD | NM_001270965.2 | c.*187C>G | 3_prime_UTR_variant | Exon 18 of 18 | NP_001257894.1 | |||
PSD | NM_001270966.2 | c.*187C>G | 3_prime_UTR_variant | Exon 18 of 18 | NP_001257895.1 | |||
PSD | NR_073110.2 | n.1554C>G | non_coding_transcript_exon_variant | Exon 8 of 8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PSD | ENST00000020673 | c.*187C>G | 3_prime_UTR_variant | Exon 17 of 17 | 1 | NM_002779.5 | ENSP00000020673.5 | |||
PSD | ENST00000406432 | c.*187C>G | 3_prime_UTR_variant | Exon 18 of 18 | 1 | ENSP00000384830.1 | ||||
PSD | ENST00000611678 | c.*187C>G | 3_prime_UTR_variant | Exon 18 of 18 | 1 | ENSP00000481250.1 |
Frequencies
GnomAD3 genomes Cov.: 28
GnomAD3 genomes
Cov.:
28
GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0AN: 169066Hom.: 0 Cov.: 4 AF XY: 0.00 AC XY: 0AN XY: 86488
GnomAD4 exome
Data not reliable, filtered out with message: AC0
AF:
AC:
0
AN:
169066
Hom.:
Cov.:
4
AF XY:
AC XY:
0
AN XY:
86488
Gnomad4 AFR exome
AF:
Gnomad4 AMR exome
AF:
Gnomad4 ASJ exome
AF:
Gnomad4 EAS exome
AF:
Gnomad4 SAS exome
AF:
Gnomad4 FIN exome
AF:
Gnomad4 NFE exome
AF:
Gnomad4 OTH exome
AF:
GnomAD4 genome Cov.: 28
GnomAD4 genome
Cov.:
28
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at