chr17-34577567-C-T

Variant names:

• chr17-34577567-C-T
• rs887230
• ENST00000623254.2:n.565G>A

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000623254.2(TMEM132E-DT):​n.565G>A 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 0.841 in 1,367,654 control chromosomes in the GnomAD database, including 484,358 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 0.85 (54655 hom., cov: 32)
  • Exomes 𝑓: 0.84 (429703 hom.)
• Consequence: TMEM132E-DT ENST00000623254.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0720
• Publications: 23 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (REVEL=0.046).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.852 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000623254.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TMEM132E-DT	NR_160787.1		n.553G>A		non_coding_transcript_exon	Exon 2 of 2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TMEM132E-DT	ENST00000623254.2	TSL:1	n.565G>A		non_coding_transcript_exon	Exon 2 of 2
	TMEM132E-DT	ENST00000661426.1		n.333G>A		non_coding_transcript_exon	Exon 2 of 3
	TMEM132E-DT	ENST00000795678.1		n.552G>A		non_coding_transcript_exon	Exon 2 of 3

Frequencies

GnomAD3 genomes AF: 0.846 AC: 128732 AN: 152084 Hom.: 54594 Cov.: 32

Gnomad AFR AF: 0.859

Gnomad AMI AF: 0.879

Gnomad AMR AF: 0.821

Gnomad ASJ AF: 0.803

Gnomad EAS AF: 0.766

Gnomad SAS AF: 0.714

Gnomad FIN AF: 0.919

Gnomad MID AF: 0.788

Gnomad NFE AF: 0.851

Gnomad OTH AF: 0.840

GnomAD2 exomes AF: 0.824 AC: 203336 AN: 246788 AF XY: 0.820

Gnomad AFR exome AF: 0.859

Gnomad AMR exome AF: 0.815

Gnomad ASJ exome AF: 0.812

Gnomad EAS exome AF: 0.758

Gnomad FIN exome AF: 0.911

Gnomad NFE exome AF: 0.845

Gnomad OTH exome AF: 0.828

GnomAD4 exome AF: 0.840 AC: 1020734 AN: 1215452 Hom.: 429703 Cov.: 60 AF XY: 0.836 AC XY: 503527 AN XY: 602372

African (AFR) AF: 0.862 AC: 22668 AN: 26300

American (AMR) AF: 0.817 AC: 30431 AN: 37268

Ashkenazi Jewish (ASJ) AF: 0.816 AC: 13786 AN: 16890

East Asian (EAS) AF: 0.766 AC: 12859 AN: 16796

South Asian (SAS) AF: 0.730 AC: 60710 AN: 83212

European-Finnish (FIN) AF: 0.908 AC: 29574 AN: 32586

Middle Eastern (MID) AF: 0.800 AC: 3576 AN: 4472

European-Non Finnish (NFE) AF: 0.850 AC: 810653 AN: 953902

Other (OTH) AF: 0.829 AC: 36477 AN: 44026

GnomAD4 genome AF: 0.847 AC: 128853 AN: 152202 Hom.: 54655 Cov.: 32 AF XY: 0.847 AC XY: 63048 AN XY: 74418

African (AFR) AF: 0.859 AC: 35669 AN: 41508

American (AMR) AF: 0.821 AC: 12564 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.803 AC: 2789 AN: 3472

East Asian (EAS) AF: 0.765 AC: 3963 AN: 5178

South Asian (SAS) AF: 0.715 AC: 3434 AN: 4806

European-Finnish (FIN) AF: 0.919 AC: 9764 AN: 10622

Middle Eastern (MID) AF: 0.789 AC: 232 AN: 294

European-Non Finnish (NFE) AF: 0.851 AC: 57858 AN: 68000

Other (OTH) AF: 0.841 AC: 1780 AN: 2116

Alfa AF: 0.840 Hom.: 200198

Bravo AF: 0.840

Asia WGS AF: 0.729 AC: 2535 AN: 3478

EpiCase AF: 0.835

EpiControl AF: 0.835

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	2.1
DANN	Benign	0.41
PhyloP100		-0.072
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs887230; hg19: chr17-32904586; COSMIC: COSV58698843;