GeneBe

17-34579902-G-GAGCGGGAGCCGATGCCCGGCAGCATCGAGACAGCGGGCGAACGGGCGTCCGGGGACAGGGTGGGGGCGGCGGGGAGGAGGCGTCGGAGACTCTGAACCCCAGAAAAGTTCAAGGTTTGTGCAGGTTCCCCCAGGGAAGGCGAGGAGCGAGGCGGGGCAGCGCGCCTCTCTGCCGAGACAGCGAGACCTTAGCGGGGTGGCCCGGAGCTGCCGTGAGCTGCAGGAGCCCCTCTGCATCTTACAGCGTTTATGGTCATCAAGCTGGAGTCGACGTCCTGGGCAGGAAGGGCTCGGGGCAGGGCGCATTAGCCGGCTTTCTCGCTCCCTCGCTTCTCCAAGCCCCATCTACATGGGGCAGCCCGTTCTGGCCGCGCCACCCTTGCCCCAGCCGCCGAGCGGCTGCCTGGGCAGGAGGCGCTGAGCCGGCCTGTGTGGAGCCTGGGCCCTGATCCAGACTGGAGAAAGCGCGCTGGAGCGGAGGAGCGAGCCTTGCGAGGGGACAAACATCTGGCCGCCCGCCTCGGGCATCCGGTCTGGGCGTCGCCTAGGGTGGTGGCGACCGGCGTCGCCAGTTTCAGCACCGCACGGAAACTTTTCCTTCTC

Variant names:

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2

The NM_001304438.2(TMEM132E):​c.-1174_-573dupAGCGGGAGCCGATGCCCGGCAGCATCGAGACAGCGGGCGAACGGGCGTCCGGGGACAGGGTGGGGGCGGCGGGGAGGAGGCGTCGGAGACTCTGAACCCCAGAAAAGTTCAAGGTTTGTGCAGGTTCCCCCAGGGAAGGCGAGGAGCGAGGCGGGGCAGCGCGCCTCTCTGCCGAGACAGCGAGACCTTAGCGGGGTGGCCCGGAGCTGCCGTGAGCTGCAGGAGCCCCTCTGCATCTTACAGCGTTTATGGTCATCAAGCTGGAGTCGACGTCCTGGGCAGGAAGGGCTCGGGGCAGGGCGCATTAGCCGGCTTTCTCGCTCCCTCGCTTCTCCAAGCCCCATCTACATGGGGCAGCCCGTTCTGGCCGCGCCACCCTTGCCCCAGCCGCCGAGCGGCTGCCTGGGCAGGAGGCGCTGAGCCGGCCTGTGTGGAGCCTGGGCCCTGATCCAGACTGGAGAAAGCGCGCTGGAGCGGAGGAGCGAGCCTTGCGAGGGGACAAACATCTGGCCGCCCGCCTCGGGCATCCGGTCTGGGCGTCGCCTAGGGTGGTGGCGACCGGCGTCGCCAGTTTCAGCACCGCACGGAAACTTTTCCTTCTC variant causes a 5 prime UTR 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 Uncertain significance (★).

Frequency

Genomes: not found (cov: 34)

Consequence

TMEM132E
NM_001304438.2 5_prime_UTR

Scores

Not classified

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 0.539
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]

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ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 2 ACMG points.

PM2
Very rare variant in population databases, with high coverage;

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
TMEM132ENM_001304438.2 linkc.-1174_-573dupAGCGGGAGCCGATGCCCGGCAGCATCGAGACAGCGGGCGAACGGGCGTCCGGGGACAGGGTGGGGGCGGCGGGGAGGAGGCGTCGGAGACTCTGAACCCCAGAAAAGTTCAAGGTTTGTGCAGGTTCCCCCAGGGAAGGCGAGGAGCGAGGCGGGGCAGCGCGCCTCTCTGCCGAGACAGCGAGACCTTAGCGGGGTGGCCCGGAGCTGCCGTGAGCTGCAGGAGCCCCTCTGCATCTTACAGCGTTTATGGTCATCAAGCTGGAGTCGACGTCCTGGGCAGGAAGGGCTCGGGGCAGGGCGCATTAGCCGGCTTTCTCGCTCCCTCGCTTCTCCAAGCCCCATCTACATGGGGCAGCCCGTTCTGGCCGCGCCACCCTTGCCCCAGCCGCCGAGCGGCTGCCTGGGCAGGAGGCGCTGAGCCGGCCTGTGTGGAGCCTGGGCCCTGATCCAGACTGGAGAAAGCGCGCTGGAGCGGAGGAGCGAGCCTTGCGAGGGGACAAACATCTGGCCGCCCGCCTCGGGCATCCGGTCTGGGCGTCGCCTAGGGTGGTGGCGACCGGCGTCGCCAGTTTCAGCACCGCACGGAAACTTTTCCTTCTC 5_prime_UTR_variant Exon 1 of 9 ENST00000631683.2 NP_001291367.1 Q6IEE7

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
TMEM132EENST00000631683 linkc.-1174_-573dupAGCGGGAGCCGATGCCCGGCAGCATCGAGACAGCGGGCGAACGGGCGTCCGGGGACAGGGTGGGGGCGGCGGGGAGGAGGCGTCGGAGACTCTGAACCCCAGAAAAGTTCAAGGTTTGTGCAGGTTCCCCCAGGGAAGGCGAGGAGCGAGGCGGGGCAGCGCGCCTCTCTGCCGAGACAGCGAGACCTTAGCGGGGTGGCCCGGAGCTGCCGTGAGCTGCAGGAGCCCCTCTGCATCTTACAGCGTTTATGGTCATCAAGCTGGAGTCGACGTCCTGGGCAGGAAGGGCTCGGGGCAGGGCGCATTAGCCGGCTTTCTCGCTCCCTCGCTTCTCCAAGCCCCATCTACATGGGGCAGCCCGTTCTGGCCGCGCCACCCTTGCCCCAGCCGCCGAGCGGCTGCCTGGGCAGGAGGCGCTGAGCCGGCCTGTGTGGAGCCTGGGCCCTGATCCAGACTGGAGAAAGCGCGCTGGAGCGGAGGAGCGAGCCTTGCGAGGGGACAAACATCTGGCCGCCCGCCTCGGGCATCCGGTCTGGGCGTCGCCTAGGGTGGTGGCGACCGGCGTCGCCAGTTTCAGCACCGCACGGAAACTTTTCCTTCTC 5_prime_UTR_variant Exon 1 of 9 5 NM_001304438.2 ENSP00000487800.2 Q6IEE7
TMEM132EENST00000321639 linkc.-1174_-573dupAGCGGGAGCCGATGCCCGGCAGCATCGAGACAGCGGGCGAACGGGCGTCCGGGGACAGGGTGGGGGCGGCGGGGAGGAGGCGTCGGAGACTCTGAACCCCAGAAAAGTTCAAGGTTTGTGCAGGTTCCCCCAGGGAAGGCGAGGAGCGAGGCGGGGCAGCGCGCCTCTCTGCCGAGACAGCGAGACCTTAGCGGGGTGGCCCGGAGCTGCCGTGAGCTGCAGGAGCCCCTCTGCATCTTACAGCGTTTATGGTCATCAAGCTGGAGTCGACGTCCTGGGCAGGAAGGGCTCGGGGCAGGGCGCATTAGCCGGCTTTCTCGCTCCCTCGCTTCTCCAAGCCCCATCTACATGGGGCAGCCCGTTCTGGCCGCGCCACCCTTGCCCCAGCCGCCGAGCGGCTGCCTGGGCAGGAGGCGCTGAGCCGGCCTGTGTGGAGCCTGGGCCCTGATCCAGACTGGAGAAAGCGCGCTGGAGCGGAGGAGCGAGCCTTGCGAGGGGACAAACATCTGGCCGCCCGCCTCGGGCATCCGGTCTGGGCGTCGCCTAGGGTGGTGGCGACCGGCGTCGCCAGTTTCAGCACCGCACGGAAACTTTTCCTTCTC 5_prime_UTR_variant Exon 1 of 10 5 ENSP00000316532.5 A0A494BWY4

Frequencies

GnomAD3 genomes
Cov.:
34
GnomAD4 exome
Cov.:
0
GnomAD4 genome
Cov.:
34

ClinVar

Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

BRCA2-related cancer predisposition Uncertain:1
Mar 15, 2019
Department of Pathology and Laboratory Medicine, Sinai Health System
Significance: Uncertain significance
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.

Other links and lift over

hg19: chr17-32906921; API