rs200789022

Variant names:

• chr13-95552516-CG-C
• rs200789022
• NM_182848.4:c.215-7613delG

Your query was ambiguous. Multiple possible variants found:

• chr13-95552516-CG-C
• chr13-95552516-CG-CGG

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP6_Moderate BA1

The NM_182848.4(CLDN10):​c.215-7613delG variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0221 in 152,256 control chromosomes in the GnomAD database, including 128 homozygotes. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.022 (128 hom., cov: 33)
• Consequence: CLDN10 NM_182848.4 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.642
• Publications: 0 publications found

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 Gene-Disease associations (from GenCC):

• HELIX syndrome

  Inheritance: AR Classification: STRONG, MODERATE, SUPPORTIVE Submitted by: Orphanet, Ambry Genetics, Labcorp Genetics (formerly Invitae)

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP6: Variant 13-95552516-CG-C is Benign according to our data. Variant chr13-95552516-CG-C is described in ClinVar as Benign. ClinVar VariationId is 1238473.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0739 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_182848.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CLDN10	NM_182848.4		c.215-7613delG		intron	N/A	NP_878268.1	P78369-2
	CLDN10	NM_001160100.2		c.158-7613delG		intron	N/A	NP_001153572.1	P78369-3
	CLDN10	NM_006984.5	MANE Select	c.-237delG		upstream_gene	N/A	NP_008915.1	P78369-1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CLDN10	ENST00000376873.7	TSL:2	c.215-7615delG		intron	N/A	ENSP00000366069.2	P78369-2
	CLDN10	ENST00000299339.3	TSL:1 MANE Select	c.-237delG		upstream_gene	N/A	ENSP00000299339.2	P78369-1
	CLDN10	ENST00000905060.1		c.-237delG		upstream_gene	N/A	ENSP00000575119.1

Frequencies

GnomAD3 genomes AF: 0.0220 AC: 3350 AN: 152148 Hom.: 126 Cov.: 33

Gnomad AFR AF: 0.0759

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00746

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.000620

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00633

Gnomad NFE AF: 0.000706

Gnomad OTH AF: 0.0187

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

GnomAD4 genome AF: 0.0221 AC: 3368 AN: 152256 Hom.: 128 Cov.: 33 AF XY: 0.0213 AC XY: 1587 AN XY: 74446

African (AFR) AF: 0.0761 AC: 3163 AN: 41554

American (AMR) AF: 0.00745 AC: 114 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3468

East Asian (EAS) AF: 0.00 AC: 0 AN: 5158

South Asian (SAS) AF: 0.000414 AC: 2 AN: 4834

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 10612

Middle Eastern (MID) AF: 0.00680 AC: 2 AN: 294

European-Non Finnish (NFE) AF: 0.000706 AC: 48 AN: 68010

Other (OTH) AF: 0.0185 AC: 39 AN: 2112

Alfa AF: 0.0157 Hom.: 8

Bravo AF: 0.0251

Asia WGS AF: 0.00867 AC: 30 AN: 3476

ClinVar

ClinVar submissions

Significance: Benign

Revision: criteria provided, single submitter

Pathogenic	VUS	Benign	Condition
-	-	1	not provided (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		-0.64
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs200789022; hg19: chr13-96204770;