chr2-113165497-C-T

Variant names:

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

Variant summary

Our verdict is Benign. Variant got -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

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

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PSD4	ENST00000465917.1	n.211+7962C>T		intron_variant	Intron 1 of 1	2

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

Gnomad4 AFR AF: 0.576

Gnomad4 AMR AF: 0.473

Gnomad4 ASJ AF: 0.242

Gnomad4 EAS AF: 0.945

Gnomad4 SAS AF: 0.565

Gnomad4 FIN AF: 0.356

Gnomad4 NFE AF: 0.234

Gnomad4 OTH AF: 0.380

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 v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1867760; hg19: chr2-113923074;