Genetic Variant TMEM132E:c.67+22403_68-22210del (chr17-34603544-CTGCTCCTGCACAGGGATCCAGCAGGCAGAAGACACAGAGGTGTCAGGCAGCGATGCTGAGTGGACCTGGGTCTGGAGCCTCAGAGGCCATTCCTTCCCTGTGTGGGCTGTGGCAGGGTCCTCCTCTGGCCAGCTCTTCCCCCTGGGTGTTCCTGTCCTCCCCTCCCTAAGCCTTGCCTTCTCAGCCTCATGGTGGCTCCTCTGCAGTGCCTGCCACCCTCAGTGATATGCCCTTGTGGGCCTCCATCCCTGGCCATCTCAGCCATACTCACTGTCCCAGCTGCAGCTGACCACTCGTCCACCATCTCCTGTGGCTATTCCATGAGTTCCTCACTGTGGGTACCAGCCCCCTCCGCCACCAGGCCTGGTCCCT-C) – ACMG Classification: Uncertain_significance (4 pts)

Variant summary

Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PM2PP5_Moderate

The NM_001304438.2(TMEM132E):c.67+22403_68-22210del variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Pathogenic (★).

Frequency

Genomes: not found (cov: 33)

Consequence

TMEM132E
NM_001304438.2 intron

Scores

Not classified

Clinical Significance

Pathogenic criteria provided, single submitter P:1

Conservation

PhyloP100: 1.08

Variant links:

Genes affected

TMEM132E (HGNC:26991): (transmembrane protein 132E) Involved in posterior lateral line neuromast hair cell development. Predicted to be located in cell body. Implicated in autosomal recessive nonsyndromic deafness 99. [provided by Alliance of Genome Resources, Apr 2022]

TMEM132E links:

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ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 4 ACMG points.

PM2

Very rare variant in population databases, with high coverage;

PP5

Variant 17-34603544-CTGCTCCTGCACAGGGATCCAGCAGGCAGAAGACACAGAGGTGTCAGGCAGCGATGCTGAGTGGACCTGGGTCTGGAGCCTCAGAGGCCATTCCTTCCCTGTGTGGGCTGTGGCAGGGTCCTCCTCTGGCCAGCTCTTCCCCCTGGGTGTTCCTGTCCTCCCCTCCCTAAGCCTTGCCTTCTCAGCCTCATGGTGGCTCCTCTGCAGTGCCTGCCACCCTCAGTGATATGCCCTTGTGGGCCTCCATCCCTGGCCATCTCAGCCATACTCACTGTCCCAGCTGCAGCTGACCACTCGTCCACCATCTCCTGTGGCTATTCCATGAGTTCCTCACTGTGGGTACCAGCCCCCTCCGCCACCAGGCCTGGTCCCT-C is Pathogenic according to our data. Variant chr17-34603544-CTGCTCCTGCACAGGGATCCAGCAGGCAGAAGACACAGAGGTGTCAGGCAGCGATGCTGAGTGGACCTGGGTCTGGAGCCTCAGAGGCCATTCCTTCCCTGTGTGGGCTGTGGCAGGGTCCTCCTCTGGCCAGCTCTTCCCCCTGGGTGTTCCTGTCCTCCCCTCCCTAAGCCTTGCCTTCTCAGCCTCATGGTGGCTCCTCTGCAGTGCCTGCCACCCTCAGTGATATGCCCTTGTGGGCCTCCATCCCTGGCCATCTCAGCCATACTCACTGTCCCAGCTGCAGCTGACCACTCGTCCACCATCTCCTGTGGCTATTCCATGAGTTCCTCACTGTGGGTACCAGCCCCCTCCGCCACCAGGCCTGGTCCCT-C is described in ClinVar as [Pathogenic]. Clinvar id is 3778953.Status of the report is criteria_provided_single_submitter, 1 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TMEM132E	NM_001304438.2 link	c.67+22403_68-22210del		intron_variant	Intron 1 of 8	ENST00000631683.2	NP_001291367.1	Q6IEE7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TMEM132E	ENST00000631683.2 link	c.67+22402_68-22211del		intron_variant	Intron 1 of 8	5	NM_001304438.2	ENSP00000487800.2		Q6IEE7
TMEM132E	ENST00000321639.7 link	c.67+22402_68-22211del		intron_variant	Intron 1 of 9	5		ENSP00000316532.5		A0A494BWY4

Frequencies

GnomAD3 genomes

Cov.:

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

GnomAD4 genome

Cov.:

ClinVar

Significance: Pathogenic

Submissions summary: Pathogenic:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

BRCA2-related cancer predisposition

Pathogenic:1

Apr 01, 2019

Department of Pathology and Laboratory Medicine, Sinai Health System

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: research

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Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

Splicing

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

Publications

No publications associated with this variant yet.