rs2191057

Variant names:

• chr17-34564035-G-A
• rs2191057
• ENST00000795675.1:n.533+14836C>T

Your query was ambiguous. Multiple possible variants found:

• chr17-34564035-G-A
• chr17-34564035-G-C

Variant summary

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

The ENST00000795675.1(TMEM132E-DT):​n.533+14836C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.172 in 152,088 control chromosomes in the GnomAD database, including 2,388 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 0.17 (2388 hom., cov: 32)
• Consequence: TMEM132E-DT ENST00000795675.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.366
• Publications: 3 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=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.207 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000795675.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TMEM132E-DT	ENST00000795675.1		n.533+14836C>T		intron	N/A
	TMEM132E-DT	ENST00000795676.1		n.110+15044C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.172 AC: 26194 AN: 151970 Hom.: 2393 Cov.: 32

Gnomad AFR AF: 0.138

Gnomad AMI AF: 0.112

Gnomad AMR AF: 0.214

Gnomad ASJ AF: 0.202

Gnomad EAS AF: 0.216

Gnomad SAS AF: 0.216

Gnomad FIN AF: 0.134

Gnomad MID AF: 0.313

Gnomad NFE AF: 0.182

Gnomad OTH AF: 0.203

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.172 AC: 26193 AN: 152088 Hom.: 2388 Cov.: 32 AF XY: 0.173 AC XY: 12832 AN XY: 74334

African (AFR) AF: 0.137 AC: 5702 AN: 41474

American (AMR) AF: 0.214 AC: 3263 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.202 AC: 700 AN: 3468

East Asian (EAS) AF: 0.216 AC: 1115 AN: 5170

South Asian (SAS) AF: 0.214 AC: 1031 AN: 4812

European-Finnish (FIN) AF: 0.134 AC: 1416 AN: 10570

Middle Eastern (MID) AF: 0.306 AC: 90 AN: 294

European-Non Finnish (NFE) AF: 0.182 AC: 12352 AN: 68000

Other (OTH) AF: 0.200 AC: 422 AN: 2114

Alfa AF: 0.187 Hom.: 5159

Bravo AF: 0.177

Asia WGS AF: 0.212 AC: 738 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	2.2
DANN	Benign	0.64
PhyloP100		-0.37

Splicing

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

Other links and lift over

dbSNP: rs2191057; hg19: chr17-32891054;