17-34606888-G-C

Position:

• chr17-34606888-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.68-19239G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.68 in 152,050 control chromosomes in the GnomAD database, including 35,490 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 0.68 (35490 hom., cov: 32)
• Consequence: TMEM132E NM_001304438.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.24

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=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.836 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TMEM132E	NM_001304438.2	c.68-19239G>C		intron_variant		ENST00000631683.2	NP_001291367.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TMEM132E	ENST00000631683.2	c.68-19239G>C		intron_variant		5	NM_001304438.2	ENSP00000487800	P1
TMEM132E	ENST00000321639.7	c.68-19239G>C		intron_variant		5		ENSP00000316532

Frequencies

GnomAD3 genomes AF: 0.680 AC: 103365 AN: 151932 Hom.: 35443 Cov.: 32

Gnomad AFR AF: 0.733

Gnomad AMI AF: 0.639

Gnomad AMR AF: 0.747

Gnomad ASJ AF: 0.616

Gnomad EAS AF: 0.857

Gnomad SAS AF: 0.697

Gnomad FIN AF: 0.641

Gnomad MID AF: 0.633

Gnomad NFE AF: 0.629

Gnomad OTH AF: 0.686

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

GnomAD4 genome AF: 0.680 AC: 103470 AN: 152050 Hom.: 35490 Cov.: 32 AF XY: 0.684 AC XY: 50863 AN XY: 74326

Gnomad4 AFR AF: 0.733

Gnomad4 AMR AF: 0.747

Gnomad4 ASJ AF: 0.616

Gnomad4 EAS AF: 0.857

Gnomad4 SAS AF: 0.697

Gnomad4 FIN AF: 0.641

Gnomad4 NFE AF: 0.629

Gnomad4 OTH AF: 0.686

Alfa AF: 0.528 Hom.: 1386

Bravo AF: 0.690

Asia WGS AF: 0.777 AC: 2697 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.39
DANN	Benign	0.47

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.020		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: rs758408; hg19: chr17-32933907;