chr17-34577461-G-A

Position:

• chr17-34577461-G-A

Variant summary

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

The NR_160787.1(TMEM132E-DT):​n.659C>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.739 in 1,304,354 control chromosomes in the GnomAD database, including 359,553 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 0.72 (40033 hom., cov: 32)
  • Exomes 𝑓: 0.74 (319520 hom.)
• Consequence: TMEM132E-DT NR_160787.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.101

Genes affected

TMEM132E-DT (HGNC:34412): (TMEM132E divergent transcript)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.756 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TMEM132E-DT	NR_160787.1	n.659C>T		non_coding_transcript_exon_variant	2/2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TMEM132E-DT	ENST00000623254.1	n.659C>T		non_coding_transcript_exon_variant	2/2	1
TMEM132E-DT	ENST00000661426.1	n.439C>T		non_coding_transcript_exon_variant	2/3

Frequencies

GnomAD3 genomes AF: 0.722 AC: 109815 AN: 152026 Hom.: 39994 Cov.: 32

Gnomad AFR AF: 0.710

Gnomad AMI AF: 0.853

Gnomad AMR AF: 0.678

Gnomad ASJ AF: 0.683

Gnomad EAS AF: 0.510

Gnomad SAS AF: 0.511

Gnomad FIN AF: 0.793

Gnomad MID AF: 0.672

Gnomad NFE AF: 0.761

Gnomad OTH AF: 0.709

GnomAD4 exome AF: 0.741 AC: 854189 AN: 1152210 Hom.: 319520 Cov.: 30 AF XY: 0.734 AC XY: 414852 AN XY: 564978

Gnomad4 AFR exome AF: 0.707

Gnomad4 AMR exome AF: 0.689

Gnomad4 ASJ exome AF: 0.694

Gnomad4 EAS exome AF: 0.508

Gnomad4 SAS exome AF: 0.541

Gnomad4 FIN exome AF: 0.782

Gnomad4 NFE exome AF: 0.765

Gnomad4 OTH exome AF: 0.718

GnomAD4 genome AF: 0.722 AC: 109910 AN: 152144 Hom.: 40033 Cov.: 32 AF XY: 0.718 AC XY: 53366 AN XY: 74360

Gnomad4 AFR AF: 0.710

Gnomad4 AMR AF: 0.677

Gnomad4 ASJ AF: 0.683

Gnomad4 EAS AF: 0.510

Gnomad4 SAS AF: 0.511

Gnomad4 FIN AF: 0.793

Gnomad4 NFE AF: 0.761

Gnomad4 OTH AF: 0.708

Alfa AF: 0.770 Hom.: 41036

Bravo AF: 0.716

Asia WGS AF: 0.476 AC: 1661 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	2.1
DANN	Benign	0.66

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs887231; hg19: chr17-32904480; COSMIC: COSV58695512;