rs11657603

chr17-34608994-G-Achr17-34608994-G-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001304438.2(TMEM132E):c.68-17133G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.575 in 152,004 control chromosomes in the GnomAD database, including 26,008 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.58 (26008 hom., cov: 32)
• Consequence: TMEM132E NM_001304438.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.652

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 -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.7 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TMEM132E	NM_001304438.2	c.68-17133G>A		intron_variant		ENST00000631683.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TMEM132E	ENST00000631683.2	c.68-17133G>A		intron_variant		5	NM_001304438.2	P1
TMEM132E	ENST00000321639.7	c.68-17133G>A		intron_variant		5

Frequencies

GnomAD3 genomes AF: 0.575 AC: 87403 AN: 151886 Hom.: 26008 Cov.: 32

Gnomad AFR AF: 0.416

Gnomad AMI AF: 0.643

Gnomad AMR AF: 0.711

Gnomad ASJ AF: 0.608

Gnomad EAS AF: 0.667

Gnomad SAS AF: 0.592

Gnomad FIN AF: 0.634

Gnomad MID AF: 0.604

Gnomad NFE AF: 0.621

Gnomad OTH AF: 0.595

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.575 AC: 87430 AN: 152004 Hom.: 26008 Cov.: 32 AF XY: 0.578 AC XY: 42975 AN XY: 74288

Gnomad4 AFR AF: 0.416

Gnomad4 AMR AF: 0.711

Gnomad4 ASJ AF: 0.608

Gnomad4 EAS AF: 0.667

Gnomad4 SAS AF: 0.592

Gnomad4 FIN AF: 0.634

Gnomad4 NFE AF: 0.621

Gnomad4 OTH AF: 0.593

Alfa AF: 0.615 Hom.: 14128

Bravo AF: 0.575

Asia WGS AF: 0.623 AC: 2164 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
Cadd	Benign	0.72
Dann	Benign	0.41

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: rs11657603; hg19: chr17-32936013;