rs10096702

Variant summary

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

The NM_015310.4(PSD3):​c.2172+24362C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0914 in 152,234 control chromosomes in the GnomAD database, including 1,120 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 0.091 ( 1120 hom., cov: 32)

Consequence

PSD3
NM_015310.4 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.278
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]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.88).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.384 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
PSD3NM_015310.4 linkuse as main transcriptc.2172+24362C>T intron_variant ENST00000327040.13

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
PSD3ENST00000327040.13 linkuse as main transcriptc.2172+24362C>T intron_variant 1 NM_015310.4 P3Q9NYI0-2
PSD3ENST00000286485.12 linkuse as main transcriptc.570+24362C>T intron_variant 1 A1Q9NYI0-3
PSD3ENST00000523619.5 linkuse as main transcriptc.1977+24362C>T intron_variant 1 A2
PSD3ENST00000518315.5 linkuse as main transcriptc.*178+24362C>T intron_variant, NMD_transcript_variant 2

Frequencies

GnomAD3 genomes
AF:
0.0913
AC:
13890
AN:
152116
Hom.:
1115
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.128
Gnomad AMI
AF:
0.0351
Gnomad AMR
AF:
0.130
Gnomad ASJ
AF:
0.0412
Gnomad EAS
AF:
0.399
Gnomad SAS
AF:
0.192
Gnomad FIN
AF:
0.0182
Gnomad MID
AF:
0.0728
Gnomad NFE
AF:
0.0445
Gnomad OTH
AF:
0.0928
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.0914
AC:
13909
AN:
152234
Hom.:
1120
Cov.:
32
AF XY:
0.0941
AC XY:
7005
AN XY:
74438
show subpopulations
Gnomad4 AFR
AF:
0.128
Gnomad4 AMR
AF:
0.130
Gnomad4 ASJ
AF:
0.0412
Gnomad4 EAS
AF:
0.398
Gnomad4 SAS
AF:
0.192
Gnomad4 FIN
AF:
0.0182
Gnomad4 NFE
AF:
0.0444
Gnomad4 OTH
AF:
0.0961
Alfa
AF:
0.0590
Hom.:
560
Bravo
AF:
0.102
Asia WGS
AF:
0.255
AC:
887
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.88
CADD
Benign
0.51
DANN
Benign
0.21

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: rs10096702; hg19: chr8-18598597; API