17-34584149-C-T

Position:

• chr17-34584149-C-T

Variant summary

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

The NM_001304438.2(TMEM132E):​c.67+3006C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.713 in 152,160 control chromosomes in the GnomAD database, including 38,985 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 0.71 (38985 hom., cov: 34)
• Consequence: TMEM132E NM_001304438.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0240

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=-0.84).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.755 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TMEM132E	NM_001304438.2	c.67+3006C>T		intron_variant		ENST00000631683.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TMEM132E	ENST00000631683.2	c.67+3006C>T		intron_variant		5	NM_001304438.2	P1
TMEM132E	ENST00000321639.7	c.67+3006C>T		intron_variant		5

Frequencies

GnomAD3 genomes AF: 0.713 AC: 108340 AN: 152042 Hom.: 38954 Cov.: 34

Gnomad AFR AF: 0.666

Gnomad AMI AF: 0.839

Gnomad AMR AF: 0.673

Gnomad ASJ AF: 0.672

Gnomad EAS AF: 0.609

Gnomad SAS AF: 0.492

Gnomad FIN AF: 0.803

Gnomad MID AF: 0.661

Gnomad NFE AF: 0.760

Gnomad OTH AF: 0.708

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

GnomAD4 genome AF: 0.713 AC: 108426 AN: 152160 Hom.: 38985 Cov.: 34 AF XY: 0.709 AC XY: 52726 AN XY: 74402

Gnomad4 AFR AF: 0.666

Gnomad4 AMR AF: 0.672

Gnomad4 ASJ AF: 0.672

Gnomad4 EAS AF: 0.609

Gnomad4 SAS AF: 0.491

Gnomad4 FIN AF: 0.803

Gnomad4 NFE AF: 0.760

Gnomad4 OTH AF: 0.708

Alfa AF: 0.735 Hom.: 27243

Bravo AF: 0.706

Asia WGS AF: 0.508 AC: 1769 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	4.6
DANN	Benign	0.48

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: rs4795942; hg19: chr17-32911168;