rs7812358

Variant summary

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

The NM_015310.4(PSD3):​c.2929-905C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.031 in 152,084 control chromosomes in the GnomAD database, including 144 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 0.031 ( 144 hom., cov: 32)

Consequence

PSD3
NM_015310.4 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.177
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=-0.91).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0772 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
PSD3NM_015310.4 linkuse as main transcriptc.2929-905C>G intron_variant ENST00000327040.13 NP_056125.3

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
PSD3ENST00000327040.13 linkuse as main transcriptc.2929-905C>G intron_variant 1 NM_015310.4 ENSP00000324127 P3Q9NYI0-2

Frequencies

GnomAD3 genomes
AF:
0.0310
AC:
4714
AN:
151966
Hom.:
143
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0795
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.0140
Gnomad ASJ
AF:
0.00951
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.0305
Gnomad FIN
AF:
0.0413
Gnomad MID
AF:
0.0316
Gnomad NFE
AF:
0.00790
Gnomad OTH
AF:
0.0235
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.0310
AC:
4719
AN:
152084
Hom.:
144
Cov.:
32
AF XY:
0.0327
AC XY:
2435
AN XY:
74366
show subpopulations
Gnomad4 AFR
AF:
0.0794
Gnomad4 AMR
AF:
0.0140
Gnomad4 ASJ
AF:
0.00951
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.0305
Gnomad4 FIN
AF:
0.0413
Gnomad4 NFE
AF:
0.00790
Gnomad4 OTH
AF:
0.0232
Alfa
AF:
0.00588
Hom.:
0
Bravo
AF:
0.0303
Asia WGS
AF:
0.0160
AC:
55
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.91
CADD
Benign
1.9
DANN
Benign
0.56

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
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: rs7812358; hg19: chr8-18394373; API