Variant rs3809997 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1

The NM_001308210.2(TSHZ1):c.1524T>C(p.Pro508Pro) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.392 in 1,613,950 control chromosomes in the GnomAD database, including 125,877 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.39 ( 11732 hom., cov: 33)

Exomes 𝑓: 0.39 ( 114145 hom. )

Consequence

TSHZ1
NM_001308210.2 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:5

Conservation

PhyloP100: -3.29

Variant links:

Genes affected

TSHZ1 (HGNC:10669): (teashirt zinc finger homeobox 1) This gene encodes a colon cancer antigen that was defined by serological analysis of recombinant cDNA expression libraries. The encoded protein is a member of the teashirt C2H2-type zinc-finger protein family and may be involved in transcriptional regulation of developmental processes. Mutations in this gene may be associated with congenital aural atresia syndrome. [provided by RefSeq, Jan 2012]

TSHZ1 links:

TSHZ1 (HGNC:):

TSHZ1 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -21 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.91).

BP6

Variant 18-75286931-T-C is Benign according to our data. Variant chr18-75286931-T-C is described in ClinVar as [Benign]. Clinvar id is 327819.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr18-75286931-T-C is described in Lovd as [Benign].

BP7

Synonymous conserved (PhyloP=-3.29 with no splicing effect.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.406 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TSHZ1	NM_001308210.2 linkuse as main transcript	c.1524T>C	p.Pro508Pro	synonymous_variant	2/2	ENST00000580243.3	NP_001295139.1	Q6ZSZ6-1
TSHZ1	NM_005786.6 linkuse as main transcript	c.1389T>C	p.Pro463Pro	synonymous_variant	2/2		NP_005777.3	Q6ZSZ6-2A7YF73

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	UniProt
TSHZ1	ENST00000580243.3 linkuse as main transcript	c.1524T>C	p.Pro508Pro	synonymous_variant	2/2	2	NM_001308210.2	ENSP00000464391.1	Q6ZSZ6-1
TSHZ1	ENST00000322038.5 linkuse as main transcript	c.1389T>C	p.Pro463Pro	synonymous_variant	2/2	1		ENSP00000323584.5	Q6ZSZ6-2
TSHZ1	ENST00000584217.1 linkuse as main transcript	n.4068T>C		non_coding_transcript_exon_variant	1/1	6

Frequencies

GnomAD3 genomes

AF:

0.389

AC:

59146

AN:

151978

Hom.:

11725

Cov.:

show subpopulations

Gnomad AFR

AF:

0.389

Gnomad AMI

AF:

0.319

Gnomad AMR

AF:

0.387

Gnomad ASJ

AF:

0.416

Gnomad EAS

AF:

0.168

Gnomad SAS

AF:

0.381

Gnomad FIN

AF:

0.367

Gnomad MID

AF:

0.396

Gnomad NFE

AF:

0.410

Gnomad OTH

AF:

0.398

GnomAD3 exomes

AF:

0.369

AC:

92604

AN:

250962

Hom.:

17842

AF XY:

0.374

AC XY:

50841

AN XY:

135770

show subpopulations

Gnomad AFR exome

AF:

0.390

Gnomad AMR exome

AF:

0.296

Gnomad ASJ exome

AF:

0.404

Gnomad EAS exome

AF:

0.158

Gnomad SAS exome

AF:

0.387

Gnomad FIN exome

AF:

0.384

Gnomad NFE exome

AF:

0.410

Gnomad OTH exome

AF:

0.396

GnomAD4 exome

AF:

0.393

AC:

573864

AN:

1461856

Hom.:

114145

Cov.:

AF XY:

0.393

AC XY:

285692

AN XY:

727222

show subpopulations

Gnomad4 AFR exome

AF:

0.388

Gnomad4 AMR exome

AF:

0.309

Gnomad4 ASJ exome

AF:

0.408

Gnomad4 EAS exome

AF:

0.182

Gnomad4 SAS exome

AF:

0.388

Gnomad4 FIN exome

AF:

0.386

Gnomad4 NFE exome

AF:

0.404

Gnomad4 OTH exome

AF:

0.388

GnomAD4 genome

AF:

0.389

AC:

59176

AN:

152094

Hom.:

11732

Cov.:

AF XY:

0.386

AC XY:

28732

AN XY:

74342

show subpopulations

Gnomad4 AFR

AF:

0.389

Gnomad4 AMR

AF:

0.386

Gnomad4 ASJ

AF:

0.416

Gnomad4 EAS

AF:

0.168

Gnomad4 SAS

AF:

0.379

Gnomad4 FIN

AF:

0.367

Gnomad4 NFE

AF:

0.410

Gnomad4 OTH

AF:

0.403

Alfa

AF:

0.405

Hom.:

9910

Bravo

AF:

0.385

Asia WGS

AF:

0.328

AC:

1140

AN:

3478

EpiCase

AF:

0.418

EpiControl

AF:

0.421

ClinVar

Significance: Benign

Submissions summary: Benign:5

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not specified

Benign:2

Benign, no assertion criteria provided	clinical testing	Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen	-	- -
Benign, no assertion criteria provided	clinical testing	Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+	-	- -

not provided

Benign:2

Benign, criteria provided, single submitter	clinical testing	GeneDx	Nov 17, 2021	- -
Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -

Aural atresia, congenital

Benign:1

Benign, criteria provided, single submitter

clinical testing

Genome-Nilou Lab

Sep 10, 2021

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.91

CADD

Benign

0.0090

DANN

Benign

0.31

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

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

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over