rs334206

Variant names:

• chr8-19052608-G-A
• rs334206
• NM_001412866.1:c.324+31598C>T

Your query was ambiguous. Multiple possible variants found:

• chr8-19052608-G-A
• chr8-19052608-G-C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001412866.1(PSD3):​c.324+31598C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.282 in 152,150 control chromosomes in the GnomAD database, including 7,173 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 0.28 (7173 hom., cov: 32)
• Consequence: PSD3 NM_001412866.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.03
• Publications: 3 publications found

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]

PSD3 Gene-Disease associations (from GenCC):

• antecubital pterygium syndrome

  Inheritance: AD Classification: LIMITED Submitted by: ClinGen

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.558 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001412866.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PSD3	NM_001412866.1		c.324+31598C>T		intron	N/A	NP_001399795.1
	PSD3	NM_001412865.1		c.324+31598C>T		intron	N/A	NP_001399794.1
	PSD3	NM_001412868.1		c.324+31598C>T		intron	N/A	NP_001399797.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PSD3	ENST00000521475.1	TSL:2	c.324+31598C>T		intron	N/A	ENSP00000428405.1

Frequencies

GnomAD3 genomes AF: 0.282 AC: 42938 AN: 152032 Hom.: 7179 Cov.: 32

Gnomad AFR AF: 0.104

Gnomad AMI AF: 0.279

Gnomad AMR AF: 0.298

Gnomad ASJ AF: 0.265

Gnomad EAS AF: 0.577

Gnomad SAS AF: 0.299

Gnomad FIN AF: 0.351

Gnomad MID AF: 0.247

Gnomad NFE AF: 0.354

Gnomad OTH AF: 0.280

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

GnomAD4 genome AF: 0.282 AC: 42943 AN: 152150 Hom.: 7173 Cov.: 32 AF XY: 0.281 AC XY: 20925 AN XY: 74372

African (AFR) AF: 0.104 AC: 4307 AN: 41514

American (AMR) AF: 0.298 AC: 4557 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.265 AC: 919 AN: 3468

East Asian (EAS) AF: 0.575 AC: 2980 AN: 5180

South Asian (SAS) AF: 0.299 AC: 1441 AN: 4812

European-Finnish (FIN) AF: 0.351 AC: 3720 AN: 10588

Middle Eastern (MID) AF: 0.255 AC: 75 AN: 294

European-Non Finnish (NFE) AF: 0.354 AC: 24102 AN: 67990

Other (OTH) AF: 0.279 AC: 588 AN: 2106

Alfa AF: 0.315 Hom.: 1954

Bravo AF: 0.276

Asia WGS AF: 0.413 AC: 1438 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	11
DANN	Benign	0.77
PhyloP100		1.0

Splicing

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

Other links and lift over

dbSNP: rs334206; hg19: chr8-18910118;