Variant chr12-57243810-G-A 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_145064.3(STAC3):c.*2C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.28 in 1,612,394 control chromosomes in the GnomAD database, including 66,431 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.25 ( 5116 hom., cov: 32)

Exomes 𝑓: 0.28 ( 61315 hom. )

Consequence

STAC3
NM_145064.3 3_prime_UTR

Scores

Clinical Significance

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

Conservation

PhyloP100: -0.123

Variant links:

Genes affected

STAC3 (HGNC:28423): (SH3 and cysteine rich domain 3) The protein encoded by this gene is a component of the excitation-contraction coupling machinery of muscles. This protein is a member of the Stac gene family and contains an N-terminal cysteine-rich domain and two SH3 domains. Mutations in this gene are a cause of Native American myopathy. [provided by RefSeq, Nov 2013]

STAC3 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=-0.75).

BP6

Variant 12-57243810-G-A is Benign according to our data. Variant chr12-57243810-G-A is described in ClinVar as [Benign]. Clinvar id is 262568.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.411 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
STAC3	NM_145064.3 linkuse as main transcript	c.*2C>T		3_prime_UTR_variant	12/12	ENST00000332782.7	NP_659501.1

Ensembl

Gene	Transcript	HGVSc	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
STAC3	ENST00000332782.7 linkuse as main transcript	c.*2C>T	3_prime_UTR_variant	12/12	2	NM_145064.3	ENSP00000329200	P1	Q96MF2-1
STAC3	ENST00000554578.5 linkuse as main transcript	c.*2C>T	3_prime_UTR_variant	11/11	1		ENSP00000452068		Q96MF2-2
STAC3	ENST00000557176.5 linkuse as main transcript	c.*157C>T	3_prime_UTR_variant, NMD_transcript_variant	8/8	1		ENSP00000450740
STAC3	ENST00000546246.2 linkuse as main transcript	c.*2C>T	3_prime_UTR_variant	9/9	2		ENSP00000441515		Q96MF2-3

Frequencies

GnomAD3 genomes

AF:

0.249

AC:

37856

AN:

151976

Hom.:

5111

Cov.:

show subpopulations

Gnomad AFR

AF:

0.178

Gnomad AMI

AF:

0.173

Gnomad AMR

AF:

0.198

Gnomad ASJ

AF:

0.214

Gnomad EAS

AF:

0.242

Gnomad SAS

AF:

0.427

Gnomad FIN

AF:

0.362

Gnomad MID

AF:

0.114

Gnomad NFE

AF:

0.278

Gnomad OTH

AF:

0.233

GnomAD3 exomes

AF:

0.271

AC:

67649

AN:

249444

Hom.:

10214

AF XY:

0.284

AC XY:

38338

AN XY:

135186

show subpopulations

Gnomad AFR exome

AF:

0.179

Gnomad AMR exome

AF:

0.138

Gnomad ASJ exome

AF:

0.212

Gnomad EAS exome

AF:

0.262

Gnomad SAS exome

AF:

0.439

Gnomad FIN exome

AF:

0.350

Gnomad NFE exome

AF:

0.272

Gnomad OTH exome

AF:

0.255

GnomAD4 exome

AF:

0.283

AC:

413455

AN:

1460300

Hom.:

61315

Cov.:

AF XY:

0.288

AC XY:

209580

AN XY:

726466

show subpopulations

Gnomad4 AFR exome

AF:

0.171

Gnomad4 AMR exome

AF:

0.146

Gnomad4 ASJ exome

AF:

0.216

Gnomad4 EAS exome

AF:

0.242

Gnomad4 SAS exome

AF:

0.434

Gnomad4 FIN exome

AF:

0.347

Gnomad4 NFE exome

AF:

0.281

Gnomad4 OTH exome

AF:

0.278

GnomAD4 genome

AF:

0.249

AC:

37878

AN:

152094

Hom.:

5116

Cov.:

AF XY:

0.256

AC XY:

19020

AN XY:

74328

show subpopulations

Gnomad4 AFR

AF:

0.178

Gnomad4 AMR

AF:

0.198

Gnomad4 ASJ

AF:

0.214

Gnomad4 EAS

AF:

0.243

Gnomad4 SAS

AF:

0.426

Gnomad4 FIN

AF:

0.362

Gnomad4 NFE

AF:

0.278

Gnomad4 OTH

AF:

0.238

Alfa

AF:

0.259

Hom.:

8328

Bravo

AF:

0.225

Asia WGS

AF:

0.293

AC:

1020

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	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	Mar 28, 2021	- -

not specified

Benign:1

Benign, criteria provided, single submitter

clinical testing

PreventionGenetics, part of Exact Sciences

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.75

CADD

Benign

DANN

Benign

0.88

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.11

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