Variant rs1353540 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_ModerateBA1

The NR_138035.2(TSHZ3):n.393+20724G>T variant causes a intron change. The variant allele was found at a frequency of 0.718 in 152,128 control chromosomes in the GnomAD database, including 39,804 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 ( 39804 hom., cov: 33)

Consequence

TSHZ3
NR_138035.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 3.89

Variant links:

Genes affected

LINC01791 (HGNC:52581): (long intergenic non-protein coding RNA 1791)

LINC01791 links:

TSHZ3 (HGNC:30700): (teashirt zinc finger homeobox 3) This gene encodes a zinc-finger transcription factor that regulates smooth muscle cell differentiation in the developing urinary tract. Consistent with this role, mice in which this gene has been inactivated exhibit abnormal gene expression in urinary tract smooth muscle cell precursors and kidney defects including hydronephrosis. The encoded transcription factor comprises a gene silencing complex that inhibits caspase expression. Reduced expression of this gene and consequent caspase upregulation may be correlated with progression of Alzheimer's disease in human patients. [provided by RefSeq, Jul 2016]

TSHZ3 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.3).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.84 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect
TSHZ3	NR_138035.2 link	n.393+20724G>T	intron_variant
TSHZ3	NR_138036.2 link	n.394-2203G>T	intron_variant
LINC01791	NR_147209.1 link	n.519-218C>A	intron_variant

Ensembl

Gene	Transcript	HGVSc	Effect	TSL
LINC01791	ENST00000589511.1 link	n.513-218C>A	intron_variant	5
TSHZ3	ENST00000651361.1 link	n.687-2203G>T	intron_variant
LINC01791	ENST00000654096.1 link	n.197-3876C>A	intron_variant

Frequencies

GnomAD3 genomes

AF:

0.718

AC:

109190

AN:

152010

Hom.:

39746

Cov.:

show subpopulations

Gnomad AFR

AF:

0.847

Gnomad AMI

AF:

0.580

Gnomad AMR

AF:

0.726

Gnomad ASJ

AF:

0.742

Gnomad EAS

AF:

0.589

Gnomad SAS

AF:

0.688

Gnomad FIN

AF:

0.629

Gnomad MID

AF:

0.734

Gnomad NFE

AF:

0.665

Gnomad OTH

AF:

0.688

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

GnomAD4 genome

AF:

0.718

AC:

109303

AN:

152128

Hom.:

39804

Cov.:

AF XY:

0.717

AC XY:

53313

AN XY:

74366

show subpopulations

Gnomad4 AFR

AF:

0.847

Gnomad4 AMR

AF:

0.726

Gnomad4 ASJ

AF:

0.742

Gnomad4 EAS

AF:

0.589

Gnomad4 SAS

AF:

0.688

Gnomad4 FIN

AF:

0.629

Gnomad4 NFE

AF:

0.665

Gnomad4 OTH

AF:

0.686

Alfa

AF:

0.708

Hom.:

6518

Bravo

AF:

0.732

Asia WGS

AF:

0.643

AC:

2232

AN:

3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.30

CADD

Benign

DANN

Benign

0.62

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