rs1386688

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_015310.4(PSD3):​c.1635-1886G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.287 in 152,026 control chromosomes in the GnomAD database, including 8,114 homozygotes. 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: 𝑓 0.29 ( 8114 hom., cov: 33)

Consequence

PSD3
NM_015310.4 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -3.14
Variant links:
Genes affected
PSD3 (HGNC:19093): (pleckstrin and Sec7 domain containing 3) Predicted to enable guanyl-nucleotide exchange factor activity and phospholipid binding activity. Predicted to be involved in regulation of ARF protein signal transduction and regulation of catalytic activity. Predicted to be located in membrane. Predicted to be active in ruffle membrane. [provided by Alliance of Genome Resources, Apr 2022]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.99).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.524 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
PSD3NM_015310.4 linkc.1635-1886G>C intron_variant ENST00000327040.13 NP_056125.3 Q9NYI0-2B3KRC4

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
PSD3ENST00000327040.13 linkc.1635-1886G>C intron_variant 1 NM_015310.4 ENSP00000324127.8 Q9NYI0-2

Frequencies

GnomAD3 genomes
AF:
0.287
AC:
43591
AN:
151908
Hom.:
8101
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.529
Gnomad AMI
AF:
0.222
Gnomad AMR
AF:
0.225
Gnomad ASJ
AF:
0.171
Gnomad EAS
AF:
0.321
Gnomad SAS
AF:
0.180
Gnomad FIN
AF:
0.261
Gnomad MID
AF:
0.266
Gnomad NFE
AF:
0.170
Gnomad OTH
AF:
0.258
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.287
AC:
43646
AN:
152026
Hom.:
8114
Cov.:
33
AF XY:
0.290
AC XY:
21523
AN XY:
74342
show subpopulations
Gnomad4 AFR
AF:
0.529
Gnomad4 AMR
AF:
0.224
Gnomad4 ASJ
AF:
0.171
Gnomad4 EAS
AF:
0.321
Gnomad4 SAS
AF:
0.180
Gnomad4 FIN
AF:
0.261
Gnomad4 NFE
AF:
0.170
Gnomad4 OTH
AF:
0.258
Alfa
AF:
0.101
Hom.:
145
Bravo
AF:
0.298

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.99
CADD
Benign
0.052
DANN
Benign
0.42

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.010
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs1386688; hg19: chr8-18664294; API