Variant 17-34626239-G-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1

The NM_001304438.2(TMEM132E):c.180G>A(p.Glu60=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.154 in 1,593,570 control chromosomes in the GnomAD database, including 21,429 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.13 ( 1561 hom., cov: 33)

Exomes 𝑓: 0.16 ( 19868 hom. )

Consequence

TMEM132E
NM_001304438.2 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:3

Conservation

PhyloP100: 3.34

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:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -21 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.71).

BP6

Variant 17-34626239-G-A is Benign according to our data. Variant chr17-34626239-G-A is described in ClinVar as [Benign]. Clinvar id is 1277963.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=3.34 with no splicing effect.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.351 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TMEM132E	NM_001304438.2 linkuse as main transcript	c.180G>A	p.Glu60=	synonymous_variant	2/9	ENST00000631683.2	NP_001291367.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TMEM132E	ENST00000631683.2 linkuse as main transcript	c.180G>A	p.Glu60=	synonymous_variant	2/9	5	NM_001304438.2	ENSP00000487800	P1
TMEM132E	ENST00000321639.7 linkuse as main transcript	c.180G>A	p.Glu60=	synonymous_variant	2/10	5		ENSP00000316532

Frequencies

GnomAD3 genomes

AF:

0.126

AC:

19217

AN:

152104

Hom.:

1562

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0446

Gnomad AMI

AF:

0.198

Gnomad AMR

AF:

0.142

Gnomad ASJ

AF:

0.0863

Gnomad EAS

AF:

0.364

Gnomad SAS

AF:

0.267

Gnomad FIN

AF:

0.163

Gnomad MID

AF:

0.117

Gnomad NFE

AF:

0.140

Gnomad OTH

AF:

0.135

GnomAD3 exomes

AF:

0.169

AC:

35634

AN:

210750

Hom.:

3564

AF XY:

0.174

AC XY:

19907

AN XY:

114658

show subpopulations

Gnomad AFR exome

AF:

0.0414

Gnomad AMR exome

AF:

0.171

Gnomad ASJ exome

AF:

0.0892

Gnomad EAS exome

AF:

0.370

Gnomad SAS exome

AF:

0.258

Gnomad FIN exome

AF:

0.158

Gnomad NFE exome

AF:

0.136

Gnomad OTH exome

AF:

0.162

GnomAD4 exome

AF:

0.157

AC:

226023

AN:

1441348

Hom.:

19868

Cov.:

AF XY:

0.160

AC XY:

114164

AN XY:

715110

show subpopulations

Gnomad4 AFR exome

AF:

0.0377

Gnomad4 AMR exome

AF:

0.167

Gnomad4 ASJ exome

AF:

0.0902

Gnomad4 EAS exome

AF:

0.376

Gnomad4 SAS exome

AF:

0.262

Gnomad4 FIN exome

AF:

0.153

Gnomad4 NFE exome

AF:

0.146

Gnomad4 OTH exome

AF:

0.158

GnomAD4 genome

AF:

0.126

AC:

19221

AN:

152222

Hom.:

1561

Cov.:

AF XY:

0.132

AC XY:

9802

AN XY:

74420

show subpopulations

Gnomad4 AFR

AF:

0.0447

Gnomad4 AMR

AF:

0.142

Gnomad4 ASJ

AF:

0.0863

Gnomad4 EAS

AF:

0.364

Gnomad4 SAS

AF:

0.266

Gnomad4 FIN

AF:

0.163

Gnomad4 NFE

AF:

0.140

Gnomad4 OTH

AF:

0.133

Alfa

AF:

0.128

Hom.:

481

Bravo

AF:

0.121

Asia WGS

AF:

0.281

AC:

974

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:3

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:3

Benign, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Jan 31, 2024	- -
Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	Nov 12, 2018	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.71

CADD

Benign

8.0

DANN

Benign

0.96

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over