rs887231

Variant names:

• chr17-34577461-G-A
• rs887231
• ENST00000623254.2:n.671C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000623254.2(TMEM132E-DT):​n.671C>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 ENST00000623254.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.101
• Publications: 12 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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.

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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TMEM132E-DT	NR_160787.1		n.659C>T		non_coding_transcript_exon	Exon 2 of 2

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TMEM132E-DT	ENST00000623254.2	TSL:1	n.671C>T		non_coding_transcript_exon	Exon 2 of 2
	TMEM132E-DT	ENST00000661426.1		n.439C>T		non_coding_transcript_exon	Exon 2 of 3
	TMEM132E-DT	ENST00000795678.1		n.658C>T		non_coding_transcript_exon	Exon 2 of 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

African (AFR) AF: 0.707 AC: 17420 AN: 24636

American (AMR) AF: 0.689 AC: 19549 AN: 28374

Ashkenazi Jewish (ASJ) AF: 0.694 AC: 10900 AN: 15704

East Asian (EAS) AF: 0.508 AC: 6699 AN: 13184

South Asian (SAS) AF: 0.541 AC: 40978 AN: 75782

European-Finnish (FIN) AF: 0.782 AC: 22265 AN: 28480

Middle Eastern (MID) AF: 0.640 AC: 2796 AN: 4370

European-Non Finnish (NFE) AF: 0.765 AC: 703647 AN: 920004

Other (OTH) AF: 0.718 AC: 29935 AN: 41676

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

African (AFR) AF: 0.710 AC: 29464 AN: 41502

American (AMR) AF: 0.677 AC: 10357 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.683 AC: 2372 AN: 3472

East Asian (EAS) AF: 0.510 AC: 2637 AN: 5168

South Asian (SAS) AF: 0.511 AC: 2460 AN: 4814

European-Finnish (FIN) AF: 0.793 AC: 8389 AN: 10576

Middle Eastern (MID) AF: 0.682 AC: 199 AN: 292

European-Non Finnish (NFE) AF: 0.761 AC: 51761 AN: 68008

Other (OTH) AF: 0.708 AC: 1493 AN: 2108

Alfa AF: 0.763 Hom.: 72585

Bravo AF: 0.716

Asia WGS AF: 0.476 AC: 1661 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	2.1
DANN	Benign	0.66
PhyloP100		0.10
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: rs887231; hg19: chr17-32904480; COSMIC: COSV58695512;