rs7833787

chr8-18850361-A-Gchr8-18850361-A-T

Variant summary

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

The NM_015310.4(PSD3):c.1634+17313T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.446 in 152,102 control chromosomes in the GnomAD database, including 15,657 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 0.45 (15657 hom., cov: 33)
• Consequence: PSD3 NM_015310.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.342

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=-0.98).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.513 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PSD3	NM_015310.4	c.1634+17313T>C		intron_variant		ENST00000327040.13

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PSD3	ENST00000327040.13	c.1634+17313T>C		intron_variant		1	NM_015310.4	P3
PSD3	ENST00000523619.5	c.1439+17313T>C		intron_variant		1		A2
PSD3	ENST00000519851.5	c.-44+3737T>C		intron_variant		5
PSD3	ENST00000518303.5	n.239+3737T>C		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.446 AC: 67728 AN: 151984 Hom.: 15644 Cov.: 33

Gnomad AFR AF: 0.412

Gnomad AMI AF: 0.447

Gnomad AMR AF: 0.522

Gnomad ASJ AF: 0.495

Gnomad EAS AF: 0.102

Gnomad SAS AF: 0.319

Gnomad FIN AF: 0.596

Gnomad MID AF: 0.522

Gnomad NFE AF: 0.457

Gnomad OTH AF: 0.480

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

GnomAD4 genome AF: 0.446 AC: 67784 AN: 152102 Hom.: 15657 Cov.: 33 AF XY: 0.448 AC XY: 33339 AN XY: 74352

Gnomad4 AFR AF: 0.412

Gnomad4 AMR AF: 0.522

Gnomad4 ASJ AF: 0.495

Gnomad4 EAS AF: 0.102

Gnomad4 SAS AF: 0.320

Gnomad4 FIN AF: 0.596

Gnomad4 NFE AF: 0.457

Gnomad4 OTH AF: 0.476

Alfa AF: 0.412 Hom.: 3661

Bravo AF: 0.441

Asia WGS AF: 0.237 AC: 829 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
Cadd	Benign	0.091
Dann	Benign	0.47

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7833787; hg19: chr8-18707871;