11-1922375-G-A

Position:

• chr11-1922375-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_006757.4(TNNT3):​c.-18-482G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.743 in 151,928 control chromosomes in the GnomAD database, including 43,071 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as not provided (no stars).

• Frequency: Genomes: 𝑓 0.74 (43071 hom., cov: 30)
• Consequence: TNNT3 NM_006757.4 intron
• Clinical Significance: not provided no classification provided O:1
• Conservation: PhyloP100: 0.900

Genes affected

TNNT3 (HGNC:11950): (troponin T3, fast skeletal type) The binding of Ca(2+) to the trimeric troponin complex initiates the process of muscle contraction. Increased Ca(2+) concentrations produce a conformational change in the troponin complex that is transmitted to tropomyosin dimers situated along actin filaments. The altered conformation permits increased interaction between a myosin head and an actin filament which, ultimately, produces a muscle contraction. The troponin complex has protein subunits C, I, and T. Subunit C binds Ca(2+) and subunit I binds to actin and inhibits actin-myosin interaction. Subunit T binds the troponin complex to the tropomyosin complex and is also required for Ca(2+)-mediated activation of actomyosin ATPase activity. There are 3 different troponin T genes that encode tissue-specific isoforms of subunit T for fast skeletal-, slow skeletal-, and cardiac-muscle. This gene encodes fast skeletal troponin T protein; also known as troponin T type 3. Alternative splicing results in multiple transcript variants encoding additional distinct troponin T type 3 isoforms. A developmentally regulated switch between fetal/neonatal and adult troponin T type 3 isoforms occurs. Additional splice variants have been described but their biological validity has not been established. Mutations in this gene may cause distal arthrogryposis multiplex congenita type 2B (DA2B). [provided by RefSeq, Oct 2009]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.907 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TNNT3	NM_006757.4	c.-18-482G>A		intron_variant		ENST00000278317.11

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TNNT3	ENST00000278317.11	c.-18-482G>A		intron_variant		5	NM_006757.4	A2

Frequencies

GnomAD3 genomes AF: 0.743 AC: 112830 AN: 151810 Hom.: 43060 Cov.: 30

Gnomad AFR AF: 0.556

Gnomad AMI AF: 0.807

Gnomad AMR AF: 0.833

Gnomad ASJ AF: 0.858

Gnomad EAS AF: 0.929

Gnomad SAS AF: 0.913

Gnomad FIN AF: 0.759

Gnomad MID AF: 0.864

Gnomad NFE AF: 0.800

Gnomad OTH AF: 0.770

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.743 AC: 112886 AN: 151928 Hom.: 43071 Cov.: 30 AF XY: 0.748 AC XY: 55495 AN XY: 74240

Gnomad4 AFR AF: 0.556

Gnomad4 AMR AF: 0.833

Gnomad4 ASJ AF: 0.858

Gnomad4 EAS AF: 0.929

Gnomad4 SAS AF: 0.913

Gnomad4 FIN AF: 0.759

Gnomad4 NFE AF: 0.800

Gnomad4 OTH AF: 0.765

Alfa AF: 0.797 Hom.: 47176

Bravo AF: 0.736

Asia WGS AF: 0.856 AC: 2976 AN: 3478

ClinVar

Significance: not provided

Submissions summary: Other:1

Revision: no classification provided

Submissions by phenotype

not provided Other:1

not provided, no classification provided

curation

Leiden Muscular Dystrophy (TNNT3)

Mar 18, 2012

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Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	6.9
DANN	Benign	0.47

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

Other links and lift over

dbSNP: rs1398256; hg19: chr11-1943605;