rs1038848

Variant names:

• chr8-18921327-T-C
• rs1038848
• NM_015310.4:c.130+14707A>G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_015310.4(PSD3):​c.130+14707A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.541 in 152,076 control chromosomes in the GnomAD database, including 23,349 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 0.54 (23349 hom., cov: 33)
• Consequence: PSD3 NM_015310.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.12

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.673 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PSD3	NM_015310.4	c.130+14707A>G		intron_variant	Intron 2 of 15	ENST00000327040.13	NP_056125.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PSD3	ENST00000327040.13	c.130+14707A>G		intron_variant	Intron 2 of 15	1	NM_015310.4	ENSP00000324127.8

Frequencies

GnomAD3 genomes AF: 0.541 AC: 82243 AN: 151958 Hom.: 23350 Cov.: 33

Gnomad AFR AF: 0.360

Gnomad AMI AF: 0.556

Gnomad AMR AF: 0.543

Gnomad ASJ AF: 0.596

Gnomad EAS AF: 0.692

Gnomad SAS AF: 0.593

Gnomad FIN AF: 0.712

Gnomad MID AF: 0.611

Gnomad NFE AF: 0.605

Gnomad OTH AF: 0.565

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.541 AC: 82267 AN: 152076 Hom.: 23349 Cov.: 33 AF XY: 0.548 AC XY: 40753 AN XY: 74330

Gnomad4 AFR AF: 0.360

Gnomad4 AMR AF: 0.543

Gnomad4 ASJ AF: 0.596

Gnomad4 EAS AF: 0.692

Gnomad4 SAS AF: 0.592

Gnomad4 FIN AF: 0.712

Gnomad4 NFE AF: 0.605

Gnomad4 OTH AF: 0.561

Alfa AF: 0.588 Hom.: 13925

Bravo AF: 0.520

Asia WGS AF: 0.604 AC: 2100 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.15
DANN	Benign	0.35

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1038848; hg19: chr8-18778837;