17-34533545-A-G

Variant names:

• chr17-34533545-A-G
• rs917500
• ENST00000795675.1:n.534-30966T>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.534-30966T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.247 in 152,070 control chromosomes in the GnomAD database, including 4,778 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 0.25 (4778 hom., cov: 32)
• Consequence: TMEM132E-DT ENST00000795675.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.447
• Publications: 2 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=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.307 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TMEM132E-DT	ENST00000795675.1	n.534-30966T>C		intron_variant	Intron 1 of 1
TMEM132E-DT	ENST00000795676.1	n.111-30966T>C		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.247 AC: 37599 AN: 151954 Hom.: 4779 Cov.: 32

Gnomad AFR AF: 0.240

Gnomad AMI AF: 0.174

Gnomad AMR AF: 0.240

Gnomad ASJ AF: 0.211

Gnomad EAS AF: 0.274

Gnomad SAS AF: 0.322

Gnomad FIN AF: 0.255

Gnomad MID AF: 0.241

Gnomad NFE AF: 0.248

Gnomad OTH AF: 0.247

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

GnomAD4 genome AF: 0.247 AC: 37618 AN: 152070 Hom.: 4778 Cov.: 32 AF XY: 0.249 AC XY: 18496 AN XY: 74340

African (AFR) AF: 0.240 AC: 9939 AN: 41470

American (AMR) AF: 0.240 AC: 3670 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.211 AC: 731 AN: 3470

East Asian (EAS) AF: 0.275 AC: 1422 AN: 5176

South Asian (SAS) AF: 0.320 AC: 1546 AN: 4824

European-Finnish (FIN) AF: 0.255 AC: 2687 AN: 10556

Middle Eastern (MID) AF: 0.238 AC: 70 AN: 294

European-Non Finnish (NFE) AF: 0.248 AC: 16882 AN: 67986

Other (OTH) AF: 0.244 AC: 513 AN: 2106

Alfa AF: 0.244 Hom.: 8013

Bravo AF: 0.246

Asia WGS AF: 0.293 AC: 1022 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.41
DANN	Benign	0.50
PhyloP100		-0.45

Splicing

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

Other links and lift over

dbSNP: rs917500; hg19: chr17-32860564;