rs79263247

Variant names:

• chr17-34581017-C-A
• rs79263247
• NM_001304438.2:c.-60C>A

Your query was ambiguous. Multiple possible variants found:

• chr17-34581017-C-A
• chr17-34581017-C-T

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2 BP4_Moderate

The NM_001304438.2(TMEM132E):​c.-60C>A variant causes a 5 prime UTR premature start codon gain change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000278 in 1,294,370 control chromosomes in the GnomAD database, with no homozygous occurrence. 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: not found (cov: 35)
  • Exomes 𝑓: 0.000028 (0 hom.)
• Consequence: TMEM132E NM_001304438.2 5_prime_UTR_premature_start_codon_gain
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0710

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 Uncertain_significance. Variant got 0 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.19).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TMEM132E	NM_001304438.2	c.-60C>A		5_prime_UTR_premature_start_codon_gain_variant	Exon 1 of 9	ENST00000631683.2	NP_001291367.1
TMEM132E	NM_001304438.2	c.-60C>A		5_prime_UTR_variant	Exon 1 of 9	ENST00000631683.2	NP_001291367.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TMEM132E	ENST00000631683	c.-60C>A		5_prime_UTR_premature_start_codon_gain_variant	Exon 1 of 9	5	NM_001304438.2	ENSP00000487800.2
TMEM132E	ENST00000631683	c.-60C>A		5_prime_UTR_variant	Exon 1 of 9	5	NM_001304438.2	ENSP00000487800.2
TMEM132E	ENST00000321639	c.-60C>A		5_prime_UTR_premature_start_codon_gain_variant	Exon 1 of 10	5		ENSP00000316532.5
TMEM132E	ENST00000321639	c.-60C>A		5_prime_UTR_variant	Exon 1 of 10	5		ENSP00000316532.5

Frequencies

GnomAD3 genomes Cov.: 35

GnomAD4 exome AF: 0.0000278 AC: 36 AN: 1294370 Hom.: 0 Cov.: 19 AF XY: 0.0000250 AC XY: 16 AN XY: 640946

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.0000356

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome Cov.: 35

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.19
CADD	Benign	13
DANN	Benign	0.96

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: rs79263247; hg19: chr17-32908036;