rs45576939

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2

The NM_001276345.2(TNNT2):​c.98-81G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000905 in 1,453,432 control chromosomes in the GnomAD database, including 21 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).

Frequency

Genomes: 𝑓 0.00097 ( 3 hom., cov: 32)
Exomes 𝑓: 0.00090 ( 18 hom. )

Consequence

TNNT2
NM_001276345.2 intron

Scores

2

Clinical Significance

Benign/Likely benign criteria provided, multiple submitters, no conflicts B:8

Conservation

PhyloP100: -0.280
Variant links:
Genes affected
TNNT2 (HGNC:11949): (troponin T2, cardiac type) This gene encodes the cardiac isoform of troponin T. The encoded protein is the tropomyosin-binding subunit of the troponin complex, which is located on the thin filament of striated muscles and regulates muscle contraction in response to alterations in intracellular calcium ion concentration. Mutations in this gene have been associated with familial hypertrophic cardiomyopathy as well as with dilated cardiomyopathy. [provided by RefSeq, May 2022]

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=-0.93).
BP6
Variant 1-201368308-C-T is Benign according to our data. Variant chr1-201368308-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 238204.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr1-201368308-C-T is described in Lovd as [Likely_benign].
BS1
Variant frequency is greater than expected in population eas. gnomad4 allele frequency = 0.000966 (147/152230) while in subpopulation EAS AF= 0.0106 (55/5182). AF 95% confidence interval is 0.00837. There are 3 homozygotes in gnomad4. There are 65 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
High AC in GnomAd4 at 147 AD gene.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
TNNT2NM_001276345.2 linkuse as main transcriptc.98-81G>A intron_variant ENST00000656932.1 NP_001263274.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
TNNT2ENST00000656932.1 linkuse as main transcriptc.98-81G>A intron_variant NM_001276345.2 ENSP00000499593 A2P45379-1

Frequencies

GnomAD3 genomes
AF:
0.000934
AC:
142
AN:
152112
Hom.:
2
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.000604
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00144
Gnomad ASJ
AF:
0.000865
Gnomad EAS
AF:
0.0106
Gnomad SAS
AF:
0.00435
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.000147
Gnomad OTH
AF:
0.00287
GnomAD4 exome
AF:
0.000898
AC:
1169
AN:
1301202
Hom.:
18
Cov.:
18
AF XY:
0.000946
AC XY:
618
AN XY:
652938
show subpopulations
Gnomad4 AFR exome
AF:
0.000264
Gnomad4 AMR exome
AF:
0.000291
Gnomad4 ASJ exome
AF:
0.00141
Gnomad4 EAS exome
AF:
0.0129
Gnomad4 SAS exome
AF:
0.00347
Gnomad4 FIN exome
AF:
0.0000407
Gnomad4 NFE exome
AF:
0.000176
Gnomad4 OTH exome
AF:
0.00297
GnomAD4 genome
AF:
0.000966
AC:
147
AN:
152230
Hom.:
3
Cov.:
32
AF XY:
0.000873
AC XY:
65
AN XY:
74414
show subpopulations
Gnomad4 AFR
AF:
0.000602
Gnomad4 AMR
AF:
0.00144
Gnomad4 ASJ
AF:
0.000865
Gnomad4 EAS
AF:
0.0106
Gnomad4 SAS
AF:
0.00436
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.000147
Gnomad4 OTH
AF:
0.00521
Alfa
AF:
0.000371
Hom.:
0
Bravo
AF:
0.000665
Asia WGS
AF:
0.0330
AC:
114
AN:
3478

ClinVar

Significance: Benign/Likely benign
Submissions summary: Benign:8
Revision: criteria provided, multiple submitters, no conflicts
LINK: link

Submissions by phenotype

not provided Benign:4
Likely benign, no assertion criteria providedclinical testingGenome Diagnostics Laboratory, University Medical Center Utrecht-- -
Likely benign, no assertion criteria providedclinical testingJoint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+-- -
Benign, criteria provided, single submitterclinical testingCeGaT Center for Human Genetics TuebingenNov 01, 2024TNNT2: BS1, BS2 -
Benign, criteria provided, single submitterclinical testingARUP Laboratories, Molecular Genetics and Genomics, ARUP LaboratoriesAug 25, 2020- -
Dilated cardiomyopathy 1D Benign:1
Benign, criteria provided, single submitterclinical testingGenome-Nilou LabApr 11, 2023- -
Cardiomyopathy, familial restrictive, 3 Benign:1
Benign, criteria provided, single submitterclinical testingGenome-Nilou LabApr 11, 2023- -
Hypertrophic cardiomyopathy 2 Benign:1
Benign, criteria provided, single submitterclinical testingGenome-Nilou LabApr 11, 2023- -
Dilated cardiomyopathy 1D;C1861864:Hypertrophic cardiomyopathy 2;C2676271:Cardiomyopathy, familial restrictive, 3 Benign:1
Likely benign, criteria provided, single submitterclinical testingLabcorp Genetics (formerly Invitae), LabcorpJan 17, 2024- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.93
CADD
Benign
1.6
DANN
Benign
0.61

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.

Other links and lift over

dbSNP: rs45576939; hg19: chr1-201337436; COSMIC: COSV52662911; COSMIC: COSV52662911; API