Variant 12-57246837-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -19 ACMG points: 0P and 19B. BP4_ModerateBP6_Very_StrongBP7BA1

The NM_145064.3(STAC3):c.570G>A(p.Lys190Lys) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00933 in 1,613,976 control chromosomes in the GnomAD database, including 209 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.0089 ( 22 hom., cov: 31)

Exomes 𝑓: 0.0094 ( 187 hom. )

Consequence

STAC3
NM_145064.3 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:4

Conservation

PhyloP100: 0.971

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:

STAC3 (HGNC:):

STAC3 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -19 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.32).

BP6

Variant 12-57246837-C-T is Benign according to our data. Variant chr12-57246837-C-T is described in ClinVar as [Benign]. Clinvar id is 262575.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=0.971 with no splicing effect.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.0662 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.570G>A	p.Lys190Lys	synonymous_variant	6/12	ENST00000332782.7	NP_659501.1	Q96MF2-1A0A024RB38

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
STAC3	ENST00000332782.7 linkuse as main transcript	c.570G>A	p.Lys190Lys	synonymous_variant	6/12	2	NM_145064.3	ENSP00000329200.2		Q96MF2-1

Frequencies

GnomAD3 genomes

AF:

0.00894

AC:

1360

AN:

152174

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00910

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00170

Gnomad ASJ

AF:

0.00231

Gnomad EAS

AF:

0.0723

Gnomad SAS

AF:

0.0215

Gnomad FIN

AF:

0.00104

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00657

Gnomad OTH

AF:

0.00574

GnomAD3 exomes

AF:

0.0109

AC:

2732

AN:

251472

Hom.:

AF XY:

0.0111

AC XY:

1508

AN XY:

135910

show subpopulations

Gnomad AFR exome

AF:

0.00837

Gnomad AMR exome

AF:

0.00162

Gnomad ASJ exome

AF:

0.00446

Gnomad EAS exome

AF:

0.0664

Gnomad SAS exome

AF:

0.0177

Gnomad FIN exome

AF:

0.00189

Gnomad NFE exome

AF:

0.00575

Gnomad OTH exome

AF:

0.00635

GnomAD4 exome

AF:

0.00937

AC:

13699

AN:

1461684

Hom.:

187

Cov.:

AF XY:

0.00952

AC XY:

6923

AN XY:

727148

show subpopulations

Gnomad4 AFR exome

AF:

0.00965

Gnomad4 AMR exome

AF:

0.00148

Gnomad4 ASJ exome

AF:

0.00574

Gnomad4 EAS exome

AF:

0.0727

Gnomad4 SAS exome

AF:

0.0185

Gnomad4 FIN exome

AF:

0.00155

Gnomad4 NFE exome

AF:

0.00710

Gnomad4 OTH exome

AF:

0.0108

GnomAD4 genome

AF:

0.00894

AC:

1362

AN:

152292

Hom.:

Cov.:

AF XY:

0.00996

AC XY:

742

AN XY:

74464

show subpopulations

Gnomad4 AFR

AF:

0.00912

Gnomad4 AMR

AF:

0.00170

Gnomad4 ASJ

AF:

0.00231

Gnomad4 EAS

AF:

0.0722

Gnomad4 SAS

AF:

0.0218

Gnomad4 FIN

AF:

0.00104

Gnomad4 NFE

AF:

0.00657

Gnomad4 OTH

AF:

0.00568

Alfa

AF:

0.00692

Hom.:

Bravo

AF:

0.00938

Asia WGS

AF:

0.0510

AC:

177

AN:

3478

EpiCase

AF:

0.00649

EpiControl

AF:

0.00563

ClinVar

Significance: Benign

Submissions summary: Benign:4

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	Apr 12, 2021	- -

not specified

Benign:1

Benign, criteria provided, single submitter

clinical testing

PreventionGenetics, part of Exact Sciences

- -

Bailey-Bloch congenital myopathy

Benign:1

Benign, criteria provided, single submitter

clinical testing

Labcorp Genetics (formerly Invitae), Labcorp

Jan 31, 2024

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.32

CADD

Benign

DANN

Benign

0.83

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