Variant 1-58576329-G-A 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_002353.3(TACSTD2):c.828C>T(p.Gly276=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0488 in 1,613,026 control chromosomes in the GnomAD database, including 2,160 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.036 ( 136 hom., cov: 33)

Exomes 𝑓: 0.050 ( 2024 hom. )

Consequence

TACSTD2
NM_002353.3 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:3

Conservation

PhyloP100: 0.119

Variant links:

Genes affected

TACSTD2 (HGNC:11530): (tumor associated calcium signal transducer 2) This intronless gene encodes a carcinoma-associated antigen. This antigen is a cell surface receptor that transduces calcium signals. Mutations of this gene have been associated with gelatinous drop-like corneal dystrophy.[provided by RefSeq, Dec 2009]

TACSTD2 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=-0.53).

BP6

Variant 1-58576329-G-A is Benign according to our data. Variant chr1-58576329-G-A is described in ClinVar as [Benign]. Clinvar id is 297765.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=0.119 with no splicing effect.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0533 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TACSTD2	NM_002353.3 linkuse as main transcript	c.828C>T	p.Gly276=	synonymous_variant	1/1	ENST00000371225.4	NP_002344.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TACSTD2	ENST00000371225.4 linkuse as main transcript	c.828C>T	p.Gly276=	synonymous_variant	1/1		NM_002353.3	ENSP00000360269	P1

Frequencies

GnomAD3 genomes

AF:

0.0362

AC:

5506

AN:

152254

Hom.:

136

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0117

Gnomad AMI

AF:

0.0219

Gnomad AMR

AF:

0.0367

Gnomad ASJ

AF:

0.0683

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.0141

Gnomad FIN

AF:

0.0278

Gnomad MID

AF:

0.0601

Gnomad NFE

AF:

0.0548

Gnomad OTH

AF:

0.0430

GnomAD3 exomes

AF:

0.0398

AC:

9808

AN:

246174

Hom.:

236

AF XY:

0.0405

AC XY:

5392

AN XY:

133136

show subpopulations

Gnomad AFR exome

AF:

0.0104

Gnomad AMR exome

AF:

0.0307

Gnomad ASJ exome

AF:

0.0626

Gnomad EAS exome

AF:

0.0000552

Gnomad SAS exome

AF:

0.0187

Gnomad FIN exome

AF:

0.0258

Gnomad NFE exome

AF:

0.0594

Gnomad OTH exome

AF:

0.0492

GnomAD4 exome

AF:

0.0502

AC:

73267

AN:

1460654

Hom.:

2024

Cov.:

AF XY:

0.0491

AC XY:

35690

AN XY:

726512

show subpopulations

Gnomad4 AFR exome

AF:

0.0108

Gnomad4 AMR exome

AF:

0.0323

Gnomad4 ASJ exome

AF:

0.0631

Gnomad4 EAS exome

AF:

0.000101

Gnomad4 SAS exome

AF:

0.0184

Gnomad4 FIN exome

AF:

0.0289

Gnomad4 NFE exome

AF:

0.0573

Gnomad4 OTH exome

AF:

0.0468

GnomAD4 genome

AF:

0.0361

AC:

5503

AN:

152372

Hom.:

136

Cov.:

AF XY:

0.0345

AC XY:

2574

AN XY:

74514

show subpopulations

Gnomad4 AFR

AF:

0.0117

Gnomad4 AMR

AF:

0.0366

Gnomad4 ASJ

AF:

0.0683

Gnomad4 EAS

AF:

0.000193

Gnomad4 SAS

AF:

0.0141

Gnomad4 FIN

AF:

0.0278

Gnomad4 NFE

AF:

0.0548

Gnomad4 OTH

AF:

0.0425

Alfa

AF:

0.0550

Hom.:

294

Bravo

AF:

0.0374

Asia WGS

AF:

0.0120

AC:

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:3

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Dec 30, 2023	- -
Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -

Gelatinous droplike corneal dystrophy

Benign:1

Benign, criteria provided, single submitter

clinical testing

Illumina Laboratory Services, Illumina

Jan 13, 2018

This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.53

CADD

Benign

DANN

Benign

0.96

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