Genetic Variant NM_001307.6:c.*343T>C (chr17-7260031-A-G) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001307.6(CLDN7):c.*343T>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.129 in 335,210 control chromosomes in the GnomAD database, including 3,378 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 0.12 ( 1294 hom., cov: 32)

Exomes 𝑓: 0.14 ( 2084 hom. )

Consequence

CLDN7
NM_001307.6 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.691

Publications

21 publications found

Variant links:

Genes affected

CLDN7 (HGNC:2049): (claudin 7) 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. Differential expression of this gene has been observed in different types of malignancies, including breast cancer, ovarian cancer, hepatocellular carcinomas, urinary tumors, prostate cancer, lung cancer, head and neck cancers, thyroid carcinomas, etc.. Alternatively spliced transcript variants encoding different isoforms have been found.[provided by RefSeq, May 2010]

CLDN7 links:

ENSG00000262302 (HGNC:):

ENSG00000262302 links:

ELP5 (HGNC:30617): (elongator acetyltransferase complex subunit 5) Predicted to contribute to tRNA binding activity. Predicted to be involved in positive regulation of cell migration and tRNA modification. Located in cytosol and nucleoplasm. Part of elongator holoenzyme complex. [provided by Alliance of Genome Resources, Apr 2022]

ELP5 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.92).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.193 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CLDN7	NM_001307.6 link	c.*343T>C		3_prime_UTR_variant	Exon 4 of 4	ENST00000360325.11	NP_001298.3
ELP5	NM_203414.3 link	c.*346A>G		downstream_gene_variant		ENST00000396628.7	NP_981959.2

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein
CLDN7	ENST00000360325.11 link	c.*343T>C	3_prime_UTR_variant	Exon 4 of 4	1	NM_001307.6	ENSP00000353475.7
ENSG00000262302	ENST00000577138.1 link	n.223+1790T>C	intron_variant	Intron 1 of 3	3		ENSP00000460571.1
ELP5	ENST00000396628.7 link	c.*346A>G	downstream_gene_variant		1	NM_203414.3	ENSP00000379869.3

Frequencies

GnomAD3 genomes

AF:

0.116

AC:

17600

AN:

152040

Hom.:

1278

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0314

Gnomad AMI

AF:

0.129

Gnomad AMR

AF:

0.179

Gnomad ASJ

AF:

0.126

Gnomad EAS

AF:

0.0886

Gnomad SAS

AF:

0.203

Gnomad FIN

AF:

0.0944

Gnomad MID

AF:

0.244

Gnomad NFE

AF:

0.151

Gnomad OTH

AF:

0.131

GnomAD4 exome

AF:

0.139

AC:

25469

AN:

183052

Hom.:

2084

Cov.:

AF XY:

0.143

AC XY:

13499

AN XY:

94450

show subpopulations

African (AFR)

AF:

0.0315

AC:

188

AN:

5962

American (AMR)

AF:

0.204

AC:

1467

AN:

7178

Ashkenazi Jewish (ASJ)

AF:

0.125

AC:

787

AN:

6314

East Asian (EAS)

AF:

0.0883

AC:

1111

AN:

12578

South Asian (SAS)

AF:

0.176

AC:

2442

AN:

13860

European-Finnish (FIN)

AF:

0.0909

AC:

838

AN:

9214

Middle Eastern (MID)

AF:

0.211

AC:

181

AN:

858

European-Non Finnish (NFE)

AF:

0.146

AC:

16928

AN:

115840

Other (OTH)

AF:

0.136

AC:

1527

AN:

11248

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1046

2093

3139

4186

5232

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

148

296

444

592

740

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.116

AC:

17644

AN:

152158

Hom.:

1294

Cov.:

AF XY:

0.117

AC XY:

8691

AN XY:

74388

show subpopulations

African (AFR)

AF:

0.0314

AC:

1307

AN:

41562

American (AMR)

AF:

0.180

AC:

2741

AN:

15258

Ashkenazi Jewish (ASJ)

AF:

0.126

AC:

438

AN:

3470

East Asian (EAS)

AF:

0.0882

AC:

457

AN:

5182

South Asian (SAS)

AF:

0.204

AC:

983

AN:

4818

European-Finnish (FIN)

AF:

0.0944

AC:

1000

AN:

10588

Middle Eastern (MID)

AF:

0.252

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.151

AC:

10232

AN:

67962

Other (OTH)

AF:

0.140

AC:

295

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.499

Heterozygous variant carriers

765

1530

2296

3061

3826

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

204

408

612

816

1020

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.147

Hom.:

1613

Bravo

AF:

0.121

Asia WGS

AF:

0.208

AC:

722

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.92

CADD

Benign

0.36

(source)

DANN

Benign

0.21

PhyloP100

-0.69

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.030

Details are displayed if max score is > 0.2

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

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over