17-34581198-G-A

Position:

• chr17-34581198-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.67+55G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.3 in 1,442,410 control chromosomes in the GnomAD database, including 68,073 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.26 (5637 hom., cov: 31)
  • Exomes 𝑓: 0.30 (62436 hom.)
• Consequence: TMEM132E NM_001304438.2 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.913

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=-0.67).
• BP6: Variant 17-34581198-G-A is Benign according to our data. Variant chr17-34581198-G-A is described in ClinVar as [Benign]. Clinvar id is 1270337.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.319 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TMEM132E	NM_001304438.2	c.67+55G>A		intron_variant		ENST00000631683.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TMEM132E	ENST00000631683.2	c.67+55G>A		intron_variant		5	NM_001304438.2	P1
TMEM132E	ENST00000321639.7	c.67+55G>A		intron_variant		5

Frequencies

GnomAD3 genomes AF: 0.258 AC: 39114 AN: 151762 Hom.: 5632 Cov.: 31

Gnomad AFR AF: 0.139

Gnomad AMI AF: 0.408

Gnomad AMR AF: 0.238

Gnomad ASJ AF: 0.282

Gnomad EAS AF: 0.253

Gnomad SAS AF: 0.125

Gnomad FIN AF: 0.374

Gnomad MID AF: 0.272

Gnomad NFE AF: 0.322

Gnomad OTH AF: 0.280

GnomAD4 exome AF: 0.305 AC: 392976 AN: 1290532 Hom.: 62436 AF XY: 0.300 AC XY: 190821 AN XY: 635372

Gnomad4 AFR exome AF: 0.133

Gnomad4 AMR exome AF: 0.181

Gnomad4 ASJ exome AF: 0.293

Gnomad4 EAS exome AF: 0.287

Gnomad4 SAS exome AF: 0.139

Gnomad4 FIN exome AF: 0.362

Gnomad4 NFE exome AF: 0.323

Gnomad4 OTH exome AF: 0.287

GnomAD4 genome AF: 0.258 AC: 39125 AN: 151878 Hom.: 5637 Cov.: 31 AF XY: 0.258 AC XY: 19172 AN XY: 74200

Gnomad4 AFR AF: 0.138

Gnomad4 AMR AF: 0.238

Gnomad4 ASJ AF: 0.282

Gnomad4 EAS AF: 0.253

Gnomad4 SAS AF: 0.125

Gnomad4 FIN AF: 0.374

Gnomad4 NFE AF: 0.322

Gnomad4 OTH AF: 0.282

Alfa AF: 0.297 Hom.: 1061

Bravo AF: 0.245

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 15, 2021

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.67
CADD	Benign	21
DANN	Benign	0.77

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: rs7212426; hg19: chr17-32908217; COSMIC: COSV58697882; COSMIC: COSV58697882;