17-7260883-C-T

Variant names:

• chr17-7260883-C-T
• rs369146758
• NM_001307.6:c.326G>A

Variant summary

Our verdict is Uncertain significance. The variant received 1 ACMG points: 2P and 1B. PM2 BP4

The NM_001307.6(CLDN7):​c.326G>A​(p.Gly109Glu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. G109A) has been classified as Uncertain significance.

• Frequency: Genomes: not found (cov: 33)
• Consequence: CLDN7 NM_001307.6 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.75
• Publications: 0 publications found

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]

ENSG00000262302 (HGNC:):

ACMG classification

Our verdict: Uncertain_significance. The variant received 1 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.32669252).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001307.6. 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
	CLDN7	NM_001307.6	MANE Select	c.326G>A	p.Gly109Glu	missense	Exon 2 of 4	NP_001298.3
	CLDN7	NM_001185022.2		c.326G>A	p.Gly109Glu	missense	Exon 3 of 5	NP_001171951.1	A0A384ME58
	CLDN7	NM_001185023.2		c.326G>A	p.Gly109Glu	missense	Exon 2 of 3	NP_001171952.1	F5H496

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CLDN7	ENST00000360325.11	TSL:1 MANE Select	c.326G>A	p.Gly109Glu	missense	Exon 2 of 4	ENSP00000353475.7	O95471-1
	CLDN7	ENST00000397317.8	TSL:1	c.326G>A	p.Gly109Glu	missense	Exon 3 of 5	ENSP00000396638.3	O95471-1
	CLDN7	ENST00000574070.5	TSL:1	c.77G>A	p.Gly26Glu	missense	Exon 1 of 3	ENSP00000460550.1	I3L3L6

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Cov.: 33

GnomAD4 genome Cov.: 33

Alfa AF: 0.00 Hom.: 0

Bravo AF: 0.00000756

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Uncertain	0.50
BayesDel_addAF	Uncertain	0.052	T
BayesDel_noAF	Benign	-0.16
CADD	Benign	22
DANN	Uncertain	1.0
DEOGEN2	Benign	0.34	T
Eigen	Benign	-0.067
Eigen_PC	Benign	0.044
FATHMM_MKL	Benign	0.65	D
LIST_S2	Benign	0.81	T
M_CAP	Benign	0.043	D
MetaRNN	Benign	0.33	T
MetaSVM	Uncertain	-0.078	T
MutationAssessor	Benign	1.3	L
PhyloP100		1.7
PrimateAI	Uncertain	0.59	T
PROVEAN	Benign	1.1	N
REVEL	Uncertain	0.45
Sift	Benign	1.0	T
Sift4G	Benign	1.0	T
Polyphen		0.97	D
Vest4		0.17
MutPred		0.55		Gain of solvent accessibility (P = 0.005)
MVP		0.94
MPC		0.53
ClinPred		0.41	T
GERP RS		4.6
PromoterAI		0.084	Neutral
Varity_R		0.30
gMVP		0.79

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

Other links and lift over

dbSNP: rs369146758; hg19: chr17-7164202;