17-34625985-G-A

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The NM_001304438.2(TMEM132E):c.68-142G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.213 in 760,202 control chromosomes in the GnomAD database, including 18,731 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.23 (4260 hom., cov: 32)
  • Exomes 𝑓: 0.21 (14471 hom.)
• Consequence: TMEM132E NM_001304438.2 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.0440

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]

ACMG classification

Verdict is Benign. Variant got -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BP6: Variant 17-34625985-G-A is Benign according to our data. Variant chr17-34625985-G-A is described in ClinVar as [Benign]. Clinvar id is 1258412.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.355 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TMEM132E	NM_001304438.2	c.68-142G>A		intron_variant		ENST00000631683.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TMEM132E	ENST00000631683.2	c.68-142G>A		intron_variant		5	NM_001304438.2	P1
TMEM132E	ENST00000321639.7	c.68-142G>A		intron_variant		5

Frequencies

GnomAD3 genomes AF: 0.227 AC: 34538 AN: 152002 Hom.: 4257 Cov.: 32

Gnomad AFR AF: 0.224

Gnomad AMI AF: 0.259

Gnomad AMR AF: 0.363

Gnomad ASJ AF: 0.274

Gnomad EAS AF: 0.234

Gnomad SAS AF: 0.274

Gnomad FIN AF: 0.158

Gnomad MID AF: 0.229

Gnomad NFE AF: 0.204

Gnomad OTH AF: 0.211

GnomAD4 exome AF: 0.209 AC: 127346 AN: 608082 Hom.: 14471 AF XY: 0.212 AC XY: 66079 AN XY: 311020

Gnomad4 AFR exome AF: 0.218

Gnomad4 AMR exome AF: 0.397

Gnomad4 ASJ exome AF: 0.268

Gnomad4 EAS exome AF: 0.216

Gnomad4 SAS exome AF: 0.270

Gnomad4 FIN exome AF: 0.167

Gnomad4 NFE exome AF: 0.196

Gnomad4 OTH exome AF: 0.218

GnomAD4 genome AF: 0.227 AC: 34570 AN: 152120 Hom.: 4260 Cov.: 32 AF XY: 0.231 AC XY: 17190 AN XY: 74382

Gnomad4 AFR AF: 0.223

Gnomad4 AMR AF: 0.363

Gnomad4 ASJ AF: 0.274

Gnomad4 EAS AF: 0.235

Gnomad4 SAS AF: 0.274

Gnomad4 FIN AF: 0.158

Gnomad4 NFE AF: 0.203

Gnomad4 OTH AF: 0.213

Alfa AF: 0.212 Hom.: 677

Bravo AF: 0.241

Asia WGS AF: 0.273 AC: 946 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

May 16, 2021

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Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
Cadd	Benign	1.9
Dann	Benign	0.55

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

Other links and lift over

dbSNP: rs62062163; hg19: chr17-32953004;