Variant 13-95578025-T-G details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_006984.5(CLDN10):c.*11T>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.328 in 1,511,044 control chromosomes in the GnomAD database, including 82,957 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.32 ( 7853 hom., cov: 32)

Exomes 𝑓: 0.33 ( 75104 hom. )

Consequence

CLDN10
NM_006984.5 3_prime_UTR

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: -0.0630

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 -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.7).

BP6

Variant 13-95578025-T-G is Benign according to our data. Variant chr13-95578025-T-G is described in ClinVar as [Benign]. Clinvar id is 1271447.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.334 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	#exon/exons	MANE	Protein	UniProt
CLDN10	NM_006984.5 linkuse as main transcript	c.*11T>G	3_prime_UTR_variant	5/5	ENST00000299339.3	NP_008915.1	P78369-1
CLDN10	NM_182848.4 linkuse as main transcript	c.*11T>G	3_prime_UTR_variant	5/5		NP_878268.1	P78369-2
CLDN10	NM_001160100.2 linkuse as main transcript	c.*11T>G	3_prime_UTR_variant	5/5		NP_001153572.1	P78369-3
CLDN10	XM_047430765.1 linkuse as main transcript	c.*11T>G	3_prime_UTR_variant	6/6		XP_047286721.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CLDN10	ENST00000299339.3 linkuse as main transcript	c.*11T>G		3_prime_UTR_variant	5/5	1	NM_006984.5	ENSP00000299339.2		P78369-1
CLDN10	ENST00000376873.7 linkuse as main transcript	c.*11T>G		3_prime_UTR_variant	5/5	2		ENSP00000366069.2		P78369-2

Frequencies

GnomAD3 genomes

AF:

0.316

AC:

48058

AN:

151998

Hom.:

7858

Cov.:

show subpopulations

Gnomad AFR

AF:

0.312

Gnomad AMI

AF:

0.353

Gnomad AMR

AF:

0.249

Gnomad ASJ

AF:

0.299

Gnomad EAS

AF:

0.150

Gnomad SAS

AF:

0.280

Gnomad FIN

AF:

0.391

Gnomad MID

AF:

0.364

Gnomad NFE

AF:

0.338

Gnomad OTH

AF:

0.306

GnomAD3 exomes

AF:

0.297

AC:

71238

AN:

239476

Hom.:

11169

AF XY:

0.303

AC XY:

39234

AN XY:

129498

show subpopulations

Gnomad AFR exome

AF:

0.312

Gnomad AMR exome

AF:

0.166

Gnomad ASJ exome

AF:

0.285

Gnomad EAS exome

AF:

0.143

Gnomad SAS exome

AF:

0.297

Gnomad FIN exome

AF:

0.375

Gnomad NFE exome

AF:

0.346

Gnomad OTH exome

AF:

0.316

GnomAD4 exome

AF:

0.330

AC:

447963

AN:

1358926

Hom.:

75104

Cov.:

AF XY:

0.329

AC XY:

224361

AN XY:

681250

show subpopulations

Gnomad4 AFR exome

AF:

0.315

Gnomad4 AMR exome

AF:

0.172

Gnomad4 ASJ exome

AF:

0.292

Gnomad4 EAS exome

AF:

0.140

Gnomad4 SAS exome

AF:

0.297

Gnomad4 FIN exome

AF:

0.371

Gnomad4 NFE exome

AF:

0.346

Gnomad4 OTH exome

AF:

0.319

GnomAD4 genome

AF:

0.316

AC:

48057

AN:

152118

Hom.:

7853

Cov.:

AF XY:

0.314

AC XY:

23375

AN XY:

74374

show subpopulations

Gnomad4 AFR

AF:

0.312

Gnomad4 AMR

AF:

0.248

Gnomad4 ASJ

AF:

0.299

Gnomad4 EAS

AF:

0.149

Gnomad4 SAS

AF:

0.279

Gnomad4 FIN

AF:

0.391

Gnomad4 NFE

AF:

0.338

Gnomad4 OTH

AF:

0.302

Alfa

AF:

0.329

Hom.:

14676

Bravo

AF:

0.303

Asia WGS

AF:

0.225

AC:

784

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
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

-0.70

CADD

Benign

7.2

DANN

Benign

0.74

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