Variant 17-34581191-T-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_001304438.2(TMEM132E):c.67+48T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.739 in 1,462,346 control chromosomes in the GnomAD database, including 402,851 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.72 ( 40145 hom., cov: 31)

Exomes 𝑓: 0.74 ( 362706 hom. )

Consequence

TMEM132E
NM_001304438.2 intron

Scores

Clinical Significance

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

Conservation

PhyloP100: 0.0270

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 -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.66).

BP6

Variant 17-34581191-T-C is Benign according to our data. Variant chr17-34581191-T-C is described in ClinVar as [Benign]. Clinvar id is 1280636.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.756 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.67+48T>C		intron_variant		ENST00000631683.2	NP_001291367.1	Q6IEE7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TMEM132E	ENST00000631683.2 linkuse as main transcript	c.67+48T>C		intron_variant		5	NM_001304438.2	ENSP00000487800.2		Q6IEE7
TMEM132E	ENST00000321639.7 linkuse as main transcript	c.67+48T>C		intron_variant		5		ENSP00000316532.5		A0A494BWY4

Frequencies

GnomAD3 genomes

AF:

0.725

AC:

109843

AN:

151610

Hom.:

40109

Cov.:

show subpopulations

Gnomad AFR

AF:

0.711

Gnomad AMI

AF:

0.853

Gnomad AMR

AF:

0.680

Gnomad ASJ

AF:

0.677

Gnomad EAS

AF:

0.543

Gnomad SAS

AF:

0.497

Gnomad FIN

AF:

0.803

Gnomad MID

AF:

0.661

Gnomad NFE

AF:

0.762

Gnomad OTH

AF:

0.710

GnomAD3 exomes

AF:

0.663

AC:

52346

AN:

78924

Hom.:

17975

AF XY:

0.657

AC XY:

28966

AN XY:

44116

show subpopulations

Gnomad AFR exome

AF:

0.666

Gnomad AMR exome

AF:

0.674

Gnomad ASJ exome

AF:

0.679

Gnomad EAS exome

AF:

0.491

Gnomad SAS exome

AF:

0.498

Gnomad FIN exome

AF:

0.790

Gnomad NFE exome

AF:

0.740

Gnomad OTH exome

AF:

0.673

GnomAD4 exome

AF:

0.740

AC:

970238

AN:

1310620

Hom.:

362706

Cov.:

AF XY:

0.734

AC XY:

473364

AN XY:

645122

show subpopulations

Gnomad4 AFR exome

AF:

0.707

Gnomad4 AMR exome

AF:

0.675

Gnomad4 ASJ exome

AF:

0.691

Gnomad4 EAS exome

AF:

0.555

Gnomad4 SAS exome

AF:

0.517

Gnomad4 FIN exome

AF:

0.795

Gnomad4 NFE exome

AF:

0.764

Gnomad4 OTH exome

AF:

0.717

GnomAD4 genome

AF:

0.725

AC:

109932

AN:

151726

Hom.:

40145

Cov.:

AF XY:

0.720

AC XY:

53386

AN XY:

74130

show subpopulations

Gnomad4 AFR

AF:

0.711

Gnomad4 AMR

AF:

0.680

Gnomad4 ASJ

AF:

0.677

Gnomad4 EAS

AF:

0.542

Gnomad4 SAS

AF:

0.496

Gnomad4 FIN

AF:

0.803

Gnomad4 NFE

AF:

0.762

Gnomad4 OTH

AF:

0.710

Alfa

AF:

0.692

Hom.:

3869

Bravo

AF:

0.718

Asia WGS

AF:

0.488

AC:

1698

AN:

3470

ClinVar

Significance: Benign

Submissions summary: Benign:3

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
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: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.66

CADD

Benign

DANN

Benign

0.28

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