4-88023359-C-T

Position:

• chr4-88023359-C-T

Variant summary

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

The NM_000297.4(PKD2):​c.709+3788C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.489 in 151,912 control chromosomes in the GnomAD database, including 18,762 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 0.49 (18762 hom., cov: 31)
• Consequence: PKD2 NM_000297.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.691

Genes affected

PKD2 (HGNC:9009): (polycystin 2, transient receptor potential cation channel) This gene encodes a member of the polycystin protein family. The encoded protein is a multi-pass membrane protein that functions as a calcium permeable cation channel, and is involved in calcium transport and calcium signaling in renal epithelial cells. This protein interacts with polycystin 1, and they may be partners in a common signaling cascade involved in tubular morphogenesis. Mutations in this gene are associated with autosomal dominant polycystic kidney disease type 2. [provided by RefSeq, Mar 2011]

PKD2 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.692 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PKD2	NM_000297.4	c.709+3788C>T		intron_variant		ENST00000237596.7	NP_000288.1
PKD2	XM_011532028.3	c.709+3788C>T		intron_variant			XP_011530330.1
PKD2	XM_011532029.2	c.-68+3788C>T		intron_variant			XP_011530331.1
PKD2	NR_156488.2	n.808+3788C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PKD2	ENST00000237596.7	c.709+3788C>T		intron_variant		1	NM_000297.4	ENSP00000237596.2
PKD2	ENST00000506727.1	n.211+3788C>T		intron_variant		4

Frequencies

GnomAD3 genomes AF: 0.489 AC: 74170 AN: 151794 Hom.: 18752 Cov.: 31

Gnomad AFR AF: 0.574

Gnomad AMI AF: 0.506

Gnomad AMR AF: 0.513

Gnomad ASJ AF: 0.398

Gnomad EAS AF: 0.712

Gnomad SAS AF: 0.599

Gnomad FIN AF: 0.452

Gnomad MID AF: 0.380

Gnomad NFE AF: 0.418

Gnomad OTH AF: 0.451

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

GnomAD4 genome AF: 0.489 AC: 74228 AN: 151912 Hom.: 18762 Cov.: 31 AF XY: 0.494 AC XY: 36705 AN XY: 74250

Gnomad4 AFR AF: 0.574

Gnomad4 AMR AF: 0.514

Gnomad4 ASJ AF: 0.398

Gnomad4 EAS AF: 0.712

Gnomad4 SAS AF: 0.597

Gnomad4 FIN AF: 0.452

Gnomad4 NFE AF: 0.418

Gnomad4 OTH AF: 0.454

Alfa AF: 0.432 Hom.: 14789

Bravo AF: 0.500

Asia WGS AF: 0.654 AC: 2272 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	1.3
DANN	Benign	0.76

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs2725227; hg19: chr4-88944511;