Variant 13-95553079-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1

The NM_006984.5(CLDN10):c.220+106C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.153 in 1,430,694 control chromosomes in the GnomAD database, including 18,864 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.12 ( 1448 hom., cov: 33)

Exomes 𝑓: 0.16 ( 17416 hom. )

Consequence

CLDN10
NM_006984.5 intron

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.0180

Variant links:

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]

CLDN10 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.76).

BP6

Variant 13-95553079-C-T is Benign according to our data. Variant chr13-95553079-C-T is described in ClinVar as [Benign]. Clinvar id is 1278746.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.186 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	#exon/exons	MANE
CLDN10	NM_006984.5 linkuse as main transcript	c.220+106C>T	intron_variant		ENST00000299339.3
CLDN10	XM_047430765.1 linkuse as main transcript	c.-2926C>T	5_prime_UTR_variant	1/6
CLDN10	NM_001160100.2 linkuse as main transcript	c.158-7053C>T	intron_variant
CLDN10	NM_182848.4 linkuse as main transcript	c.215-7053C>T	intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CLDN10	ENST00000299339.3 linkuse as main transcript	c.220+106C>T		intron_variant		1	NM_006984.5	P1	P78369-1
CLDN10	ENST00000376873.7 linkuse as main transcript	c.215-7053C>T		intron_variant		2			P78369-2

Frequencies

GnomAD3 genomes

AF:

0.117

AC:

17732

AN:

152038

Hom.:

1442

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0311

Gnomad AMI

AF:

0.0559

Gnomad AMR

AF:

0.191

Gnomad ASJ

AF:

0.0723

Gnomad EAS

AF:

0.00407

Gnomad SAS

AF:

0.130

Gnomad FIN

AF:

0.163

Gnomad MID

AF:

0.0380

Gnomad NFE

AF:

0.156

Gnomad OTH

AF:

0.112

GnomAD4 exome

AF:

0.158

AC:

201462

AN:

1278538

Hom.:

17416

AF XY:

0.157

AC XY:

98340

AN XY:

628092

show subpopulations

Gnomad4 AFR exome

AF:

0.0224

Gnomad4 AMR exome

AF:

0.271

Gnomad4 ASJ exome

AF:

0.0672

Gnomad4 EAS exome

AF:

0.00372

Gnomad4 SAS exome

AF:

0.140

Gnomad4 FIN exome

AF:

0.163

Gnomad4 NFE exome

AF:

0.168

Gnomad4 OTH exome

AF:

0.134

GnomAD4 genome

AF:

0.117

AC:

17748

AN:

152156

Hom.:

1448

Cov.:

AF XY:

0.117

AC XY:

8691

AN XY:

74378

show subpopulations

Gnomad4 AFR

AF:

0.0310

Gnomad4 AMR

AF:

0.192

Gnomad4 ASJ

AF:

0.0723

Gnomad4 EAS

AF:

0.00408

Gnomad4 SAS

AF:

0.131

Gnomad4 FIN

AF:

0.163

Gnomad4 NFE

AF:

0.156

Gnomad4 OTH

AF:

0.111

Alfa

AF:

0.0671

Hom.:

Bravo

AF:

0.119

Asia WGS

AF:

0.0580

AC:

202

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

May 11, 2021

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.76

CADD

Benign

7.1

DANN

Benign

0.85

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over