rs11995449

chr8-8702388-G-Achr8-8702388-G-C

Variant summary

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

The NM_194284.3(CLDN23):c.-11G>A variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.259 in 1,473,330 control chromosomes in the GnomAD database, including 51,707 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 0.24 (4975 hom., cov: 33)
  • Exomes 𝑓: 0.26 (46732 hom.)
• Consequence: CLDN23 NM_194284.3 5_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.463

Genes affected

CLDN23 (HGNC:17591): (claudin 23) This gene encodes a member of the claudin family. Claudins are integral membrane proteins and components of tight junction strands. Tight junction strands serve as a physical barrier to prevent solutes and water from passing freely through the paracellular space between epithelial or endothelial cell sheets, and also play critical roles in maintaining cell polarity and signal transductions. This gene is expressed in germinal center B-cells, placenta and stomach as well as in colon tumor. This gene is down-regulated in intestinal type gastric cancer. [provided by RefSeq, Aug 2010]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.76).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.428 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CLDN23	NM_194284.3	c.-11G>A		5_prime_UTR_variant	1/1	ENST00000519106.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CLDN23	ENST00000519106.2	c.-11G>A		5_prime_UTR_variant	1/1		NM_194284.3	P1

Frequencies

GnomAD3 genomes AF: 0.243 AC: 36893 AN: 152058 Hom.: 4961 Cov.: 33

Gnomad AFR AF: 0.155

Gnomad AMI AF: 0.315

Gnomad AMR AF: 0.295

Gnomad ASJ AF: 0.205

Gnomad EAS AF: 0.444

Gnomad SAS AF: 0.395

Gnomad FIN AF: 0.345

Gnomad MID AF: 0.177

Gnomad NFE AF: 0.244

Gnomad OTH AF: 0.223

GnomAD3 exomes AF: 0.308 AC: 38852 AN: 126026 Hom.: 6280 AF XY: 0.306 AC XY: 21436 AN XY: 70078

Gnomad AFR exome AF: 0.159

Gnomad AMR exome AF: 0.402

Gnomad ASJ exome AF: 0.219

Gnomad EAS exome AF: 0.443

Gnomad SAS exome AF: 0.398

Gnomad FIN exome AF: 0.350

Gnomad NFE exome AF: 0.259

Gnomad OTH exome AF: 0.309

GnomAD4 exome AF: 0.261 AC: 344297 AN: 1321154 Hom.: 46732 Cov.: 33 AF XY: 0.264 AC XY: 170641 AN XY: 646484

Gnomad4 AFR exome AF: 0.146

Gnomad4 AMR exome AF: 0.372

Gnomad4 ASJ exome AF: 0.201

Gnomad4 EAS exome AF: 0.410

Gnomad4 SAS exome AF: 0.389

Gnomad4 FIN exome AF: 0.335

Gnomad4 NFE exome AF: 0.246

Gnomad4 OTH exome AF: 0.266

GnomAD4 genome AF: 0.243 AC: 36945 AN: 152176 Hom.: 4975 Cov.: 33 AF XY: 0.251 AC XY: 18650 AN XY: 74412

Gnomad4 AFR AF: 0.156

Gnomad4 AMR AF: 0.296

Gnomad4 ASJ AF: 0.205

Gnomad4 EAS AF: 0.443

Gnomad4 SAS AF: 0.395

Gnomad4 FIN AF: 0.345

Gnomad4 NFE AF: 0.244

Gnomad4 OTH AF: 0.231

Alfa AF: 0.165 Hom.: 407

Bravo AF: 0.235

Asia WGS AF: 0.436 AC: 1514 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
Cadd	Benign	12
Dann	Benign	0.97

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: rs11995449; hg19: chr8-8559898;