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GeneBe

8-18556275-G-A

Variant summary

Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BA1

The NM_015310.4(PSD3):c.2862C>T(p.Pro954=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00272 in 1,613,814 control chromosomes in the GnomAD database, including 106 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.015 ( 52 hom., cov: 32)
Exomes 𝑓: 0.0015 ( 54 hom. )

Consequence

PSD3
NM_015310.4 synonymous

Scores

2

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -4.50
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 -15 ACMG points.

BP4
?
    BP4 - Multiple lines of computational evidence suggest no impact on gene or gene product (conservation, evolutionary, splicing impact, etc.)
Computational evidence support a benign effect (BayesDel_noAF=-1.02).
BP6
?
    BP6 - Reputable source recently reports variant as benign, but the evidence is not available to the laboratory to perform an independent evaluation
Variant 8-18556275-G-A is Benign according to our data. Variant chr8-18556275-G-A is described in ClinVar as [Benign]. Clinvar id is 719443.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
    BP7 - A synonymous (silent) variant for which splicing prediction algorithms predict no impact to the splice consensus sequence nor the creation of a new splice site AND the nucleotide is not highly conserved
Synonymous conserved (PhyloP=-4.51 with no splicing effect.
BA1
?
    BA1 - Allele frequency is >5% in Exome Sequencing Project, 1000 Genomes Project, or Exome Aggregation Consortium
GnomAdExome4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0502 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
PSD3NM_015310.4 linkuse as main transcriptc.2862C>T p.Pro954= synonymous_variant 15/16 ENST00000327040.13

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
PSD3ENST00000327040.13 linkuse as main transcriptc.2862C>T p.Pro954= synonymous_variant 15/161 NM_015310.4 P3Q9NYI0-2

Frequencies

GnomAD3 genomes
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.0146
AC:
2219
AN:
152028
Hom.:
52
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0510
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00524
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00125
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.000132
Gnomad OTH
AF:
0.00621
GnomAD3 exomes
AF:
0.00393
AC:
986
AN:
251170
Hom.:
22
AF XY:
0.00287
AC XY:
390
AN XY:
135738
show subpopulations
Gnomad AFR exome
AF:
0.0531
Gnomad AMR exome
AF:
0.00223
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.0000544
Gnomad SAS exome
AF:
0.000751
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.0000969
Gnomad OTH exome
AF:
0.00196
GnomAD4 exome
AF:
0.00148
AC:
2166
AN:
1461670
Hom.:
54
Cov.:
30
AF XY:
0.00128
AC XY:
932
AN XY:
727132
show subpopulations
Gnomad4 AFR exome
AF:
0.0522
Gnomad4 AMR exome
AF:
0.00237
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.000939
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.0000477
Gnomad4 OTH exome
AF:
0.00280
GnomAD4 genome
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.0146
AC:
2224
AN:
152144
Hom.:
52
Cov.:
32
AF XY:
0.0140
AC XY:
1041
AN XY:
74376
show subpopulations
Gnomad4 AFR
AF:
0.0510
Gnomad4 AMR
AF:
0.00523
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00125
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.000132
Gnomad4 OTH
AF:
0.00615
Alfa
AF:
0.00636
Hom.:
11
Bravo
AF:
0.0167
Asia WGS
AF:
0.00289
AC:
10
AN:
3478
EpiCase
AF:
0.00
EpiControl
AF:
0.000119

ClinVar

Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not provided Benign:1
Benign, criteria provided, single submitterclinical testingInvitaeJul 31, 2018- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-1.0
Cadd
Benign
0.15
Dann
Benign
0.52

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: rs28651847; hg19: chr8-18413785; API