Variant chr17-34577567-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NR_160787.1(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
NR_160787.1 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0720

Variant links:

Genes affected

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

TMEM132E-DT links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

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/exons	MANE	Protein	UniProt
TMEM132E-DT	NR_160787.1 linkuse as main transcript	n.553G>A		non_coding_transcript_exon_variant	2/2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TMEM132E-DT	ENST00000623254.1 linkuse as main transcript	n.553G>A		non_coding_transcript_exon_variant	2/2	1
TMEM132E-DT	ENST00000661426.1 linkuse as main transcript	n.333G>A		non_coding_transcript_exon_variant	2/3

Frequencies

GnomAD3 genomes

AF:

0.846

AC:

128732

AN:

152084

Hom.:

54594

Cov.:

show subpopulations

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

show subpopulations

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.:

AF XY:

0.836

AC XY:

503527

AN XY:

602372

show subpopulations

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.:

AF XY:

0.847

AC XY:

63048

AN XY:

74418

show subpopulations

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over