17-34577567-C-T

Variant names:

• chr17-34577567-C-T
• rs887230
• ENST00000623254.1:n.553G>A

Variant summary

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

The ENST00000623254.1(TMEM132E-DT):​n.553G>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 ENST00000623254.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0720

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=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.852 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TMEM132E-DT	NR_160787.1	n.553G>A		non_coding_transcript_exon_variant	Exon 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TMEM132E-DT	ENST00000623254.1	n.553G>A		non_coding_transcript_exon_variant	Exon 2 of 2	1
TMEM132E-DT	ENST00000661426.1	n.333G>A		non_coding_transcript_exon_variant	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

GnomAD3 exomes AF: 0.824 AC: 203336 AN: 246788 Hom.: 84302 AF XY: 0.820 AC XY: 109935 AN XY: 134120

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 SAS exome AF: 0.721

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

Gnomad4 AFR exome AF: 0.862

Gnomad4 AMR exome AF: 0.817

Gnomad4 ASJ exome AF: 0.816

Gnomad4 EAS exome AF: 0.766

Gnomad4 SAS exome AF: 0.730

Gnomad4 FIN exome AF: 0.908

Gnomad4 NFE exome AF: 0.850

Gnomad4 OTH exome AF: 0.829

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

Gnomad4 AFR AF: 0.859

Gnomad4 AMR AF: 0.821

Gnomad4 ASJ AF: 0.803

Gnomad4 EAS AF: 0.765

Gnomad4 SAS AF: 0.715

Gnomad4 FIN AF: 0.919

Gnomad4 NFE AF: 0.851

Gnomad4 OTH AF: 0.841

Alfa AF: 0.839 Hom.: 137058

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 v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	2.1
DANN	Benign	0.41

Splicing

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

Publications

LitVar

Other links and lift over

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