Variant 1-58576137-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_002353.3(TACSTD2):c.*48G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0879 in 1,596,804 control chromosomes in the GnomAD database, including 6,675 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.077 ( 489 hom., cov: 33)

Exomes 𝑓: 0.089 ( 6186 hom. )

Consequence

TACSTD2
NM_002353.3 3_prime_UTR

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: -0.525

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 -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.7).

BP6

Variant 1-58576137-C-T is Benign according to our data. Variant chr1-58576137-C-T is described in ClinVar as [Benign]. Clinvar id is 297763.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0963 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.*48G>A		3_prime_UTR_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.*48G>A		3_prime_UTR_variant	1/1		NM_002353.3	ENSP00000360269	P1

Frequencies

GnomAD3 genomes

AF:

0.0774

AC:

11779

AN:

152176

Hom.:

488

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0519

Gnomad AMI

AF:

0.124

Gnomad AMR

AF:

0.0730

Gnomad ASJ

AF:

0.100

Gnomad EAS

AF:

0.00250

Gnomad SAS

AF:

0.0574

Gnomad FIN

AF:

0.0783

Gnomad MID

AF:

0.161

Gnomad NFE

AF:

0.0983

Gnomad OTH

AF:

0.0908

GnomAD3 exomes

AF:

0.0761

AC:

17051

AN:

224032

Hom.:

732

AF XY:

0.0785

AC XY:

9472

AN XY:

120604

show subpopulations

Gnomad AFR exome

AF:

0.0528

Gnomad AMR exome

AF:

0.0514

Gnomad ASJ exome

AF:

0.101

Gnomad EAS exome

AF:

0.00165

Gnomad SAS exome

AF:

0.0626

Gnomad FIN exome

AF:

0.0819

Gnomad NFE exome

AF:

0.0990

Gnomad OTH exome

AF:

0.0938

GnomAD4 exome

AF:

0.0890

AC:

128589

AN:

1444510

Hom.:

6186

Cov.:

AF XY:

0.0893

AC XY:

64056

AN XY:

717338

show subpopulations

Gnomad4 AFR exome

AF:

0.0543

Gnomad4 AMR exome

AF:

0.0532

Gnomad4 ASJ exome

AF:

0.0996

Gnomad4 EAS exome

AF:

0.000906

Gnomad4 SAS exome

AF:

0.0631

Gnomad4 FIN exome

AF:

0.0777

Gnomad4 NFE exome

AF:

0.0966

Gnomad4 OTH exome

AF:

0.0887

GnomAD4 genome

AF:

0.0774

AC:

11788

AN:

152294

Hom.:

489

Cov.:

AF XY:

0.0752

AC XY:

5601

AN XY:

74460

show subpopulations

Gnomad4 AFR

AF:

0.0519

Gnomad4 AMR

AF:

0.0729

Gnomad4 ASJ

AF:

0.100

Gnomad4 EAS

AF:

0.00251

Gnomad4 SAS

AF:

0.0585

Gnomad4 FIN

AF:

0.0783

Gnomad4 NFE

AF:

0.0983

Gnomad4 OTH

AF:

0.0899

Alfa

AF:

0.0922

Hom.:

178

Bravo

AF:

0.0756

Asia WGS

AF:

0.0420

AC:

147

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:1

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 12, 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

-0.70

CADD

Benign

4.0

DANN

Benign

0.92

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