2-113165497-C-T

Variant names:

• chr2-113165497-C-T
• rs1867760
• ENST00000465917.1:n.211+7962C>T

Variant summary

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

The ENST00000465917.1(PSD4):​n.211+7962C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.397 in 152,160 control chromosomes in the GnomAD database, including 14,614 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 0.40 (14614 hom., cov: 32)
• Consequence: PSD4 ENST00000465917.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.712
• Publications: 2 publications found

Genes affected

PSD4 (HGNC:19096): (pleckstrin and Sec7 domain containing 4) 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. Located in ruffle membrane. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.922 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000465917.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PSD4	ENST00000465917.1	TSL:2	n.211+7962C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.397 AC: 60348 AN: 152042 Hom.: 14575 Cov.: 32

Gnomad AFR AF: 0.575

Gnomad AMI AF: 0.294

Gnomad AMR AF: 0.472

Gnomad ASJ AF: 0.242

Gnomad EAS AF: 0.945

Gnomad SAS AF: 0.566

Gnomad FIN AF: 0.356

Gnomad MID AF: 0.306

Gnomad NFE AF: 0.234

Gnomad OTH AF: 0.377

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

GnomAD4 genome AF: 0.397 AC: 60450 AN: 152160 Hom.: 14614 Cov.: 32 AF XY: 0.410 AC XY: 30503 AN XY: 74374

African (AFR) AF: 0.576 AC: 23898 AN: 41504

American (AMR) AF: 0.473 AC: 7235 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.242 AC: 840 AN: 3468

East Asian (EAS) AF: 0.945 AC: 4893 AN: 5180

South Asian (SAS) AF: 0.565 AC: 2724 AN: 4824

European-Finnish (FIN) AF: 0.356 AC: 3766 AN: 10582

Middle Eastern (MID) AF: 0.301 AC: 88 AN: 292

European-Non Finnish (NFE) AF: 0.234 AC: 15935 AN: 67992

Other (OTH) AF: 0.380 AC: 803 AN: 2112

Alfa AF: 0.179 Hom.: 377

Bravo AF: 0.414

Asia WGS AF: 0.741 AC: 2574 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	1.5
DANN	Benign	0.72
PhyloP100		-0.71

Splicing

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

Other links and lift over

dbSNP: rs1867760; hg19: chr2-113923074;