chr17-34581045-T-C
Variant summary
Our verdict is Benign. Variant got -18 ACMG points: 0P and 18B. BP4_ModerateBP6_Very_StrongBA1
The NM_001304438.2(TMEM132E):c.-32T>C variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.855 in 1,522,808 control chromosomes in the GnomAD database, including 557,625 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.89 ( 60087 hom., cov: 35)
Exomes 𝑓: 0.85 ( 497538 hom. )
Consequence
TMEM132E
NM_001304438.2 5_prime_UTR
NM_001304438.2 5_prime_UTR
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.375
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]
Genome browser will be placed here
ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -18 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.37).
BP6
?
Variant 17-34581045-T-C is Benign according to our data. Variant chr17-34581045-T-C is described in ClinVar as [Benign]. Clinvar id is 1235963.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.963 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TMEM132E | NM_001304438.2 | c.-32T>C | 5_prime_UTR_variant | 1/9 | ENST00000631683.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TMEM132E | ENST00000631683.2 | c.-32T>C | 5_prime_UTR_variant | 1/9 | 5 | NM_001304438.2 | P1 | ||
TMEM132E | ENST00000321639.7 | c.-32T>C | 5_prime_UTR_variant | 1/10 | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.886 AC: 134845AN: 152166Hom.: 60022 Cov.: 35
GnomAD3 genomes
?
AF:
AC:
134845
AN:
152166
Hom.:
Cov.:
35
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD3 exomes AF: 0.835 AC: 132298AN: 158516Hom.: 55513 AF XY: 0.832 AC XY: 74185AN XY: 89170
GnomAD3 exomes
AF:
AC:
132298
AN:
158516
Hom.:
AF XY:
AC XY:
74185
AN XY:
89170
Gnomad AFR exome
AF:
Gnomad AMR exome
AF:
Gnomad ASJ exome
AF:
Gnomad EAS exome
AF:
Gnomad SAS exome
AF:
Gnomad FIN exome
AF:
Gnomad NFE exome
AF:
Gnomad OTH exome
AF:
GnomAD4 exome AF: 0.851 AC: 1166691AN: 1370526Hom.: 497538 Cov.: 28 AF XY: 0.849 AC XY: 576167AN XY: 678706
GnomAD4 exome
AF:
AC:
1166691
AN:
1370526
Hom.:
Cov.:
28
AF XY:
AC XY:
576167
AN XY:
678706
Gnomad4 AFR exome
AF:
Gnomad4 AMR exome
AF:
Gnomad4 ASJ exome
AF:
Gnomad4 EAS exome
AF:
Gnomad4 SAS exome
AF:
Gnomad4 FIN exome
AF:
Gnomad4 NFE exome
AF:
Gnomad4 OTH exome
AF:
GnomAD4 genome ? AF: 0.886 AC: 134970AN: 152282Hom.: 60087 Cov.: 35 AF XY: 0.887 AC XY: 66040AN XY: 74458
GnomAD4 genome
?
AF:
AC:
134970
AN:
152282
Hom.:
Cov.:
35
AF XY:
AC XY:
66040
AN XY:
74458
Gnomad4 AFR
AF:
Gnomad4 AMR
AF:
Gnomad4 ASJ
AF:
Gnomad4 EAS
AF:
Gnomad4 SAS
AF:
Gnomad4 FIN
AF:
Gnomad4 NFE
AF:
Gnomad4 OTH
AF:
Alfa
AF:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
2800
AN:
3472
ClinVar
Significance: Benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Nov 12, 2018 | - - |
Hearing loss, autosomal recessive 99 Benign:1
Benign, criteria provided, single submitter | clinical testing | Genome-Nilou Lab | Sep 10, 2021 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at