13-95434226-C-T

Position:

• chr13-95434226-C-T

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The NM_182848.4(CLDN10):​c.214+179C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.58 in 151,942 control chromosomes in the GnomAD database, including 28,086 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.58 (28086 hom., cov: 30)
• Consequence: CLDN10 NM_182848.4 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.0480

Genes affected

CLDN10 (HGNC:2033): (claudin 10) 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. The expression level of this gene is associated with recurrence of primary hepatocellular carcinoma. Six alternatively spliced transcript variants encoding different isoforms have been reported, but the transcript sequences of some variants are not determined.[provided by RefSeq, Jun 2010]

ACMG classification

Verdict is Benign. Variant got -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BP6: Variant 13-95434226-C-T is Benign according to our data. Variant chr13-95434226-C-T is described in ClinVar as [Benign]. Clinvar id is 1183412.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.853 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CLDN10	NM_182848.4	c.214+179C>T		intron_variant			NP_878268.1
CLDN10	NM_001160100.2	c.157+236C>T		intron_variant			NP_001153572.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CLDN10	ENST00000376873.7	c.214+179C>T		intron_variant		2		ENSP00000366069.2

Frequencies

GnomAD3 genomes AF: 0.579 AC: 87963 AN: 151824 Hom.: 28027 Cov.: 30

Gnomad AFR AF: 0.860

Gnomad AMI AF: 0.307

Gnomad AMR AF: 0.521

Gnomad ASJ AF: 0.471

Gnomad EAS AF: 0.516

Gnomad SAS AF: 0.642

Gnomad FIN AF: 0.500

Gnomad MID AF: 0.612

Gnomad NFE AF: 0.444

Gnomad OTH AF: 0.545

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

GnomAD4 genome AF: 0.580 AC: 88091 AN: 151942 Hom.: 28086 Cov.: 30 AF XY: 0.584 AC XY: 43342 AN XY: 74240

Gnomad4 AFR AF: 0.860

Gnomad4 AMR AF: 0.521

Gnomad4 ASJ AF: 0.471

Gnomad4 EAS AF: 0.516

Gnomad4 SAS AF: 0.642

Gnomad4 FIN AF: 0.500

Gnomad4 NFE AF: 0.444

Gnomad4 OTH AF: 0.550

Alfa AF: 0.469 Hom.: 35193

Bravo AF: 0.586

Asia WGS AF: 0.630 AC: 2191 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

May 10, 2021

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	2.9
DANN	Benign	0.33

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7333503; hg19: chr13-96086480;