chr2-178536168-C-T

Variant names:

• chr2-178536168-C-T
• rs2278196
• NM_001267550.2:c.100579G>A

Variant summary

Our verdict is Benign. The variant received -20 ACMG points: 0P and 20B. BP4_Strong BP6_Very_Strong BA1

The NM_001267550.2(TTN):​c.100579G>A​(p.Val33527Ile) variant causes a missense change. The variant allele was found at a frequency of 0.0253 in 1,613,412 control chromosomes in the GnomAD database, including 1,143 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).

• Frequency:
  • Genomes: 𝑓 0.038 (193 hom., cov: 33)
  • Exomes 𝑓: 0.024 (950 hom.)
• Consequence: TTN NM_001267550.2 missense
• Clinical Significance: Benign/Likely benign criteria provided, multiple submitters, no conflicts B:21
• Conservation: PhyloP100: 4.77
• Publications: 21 publications found

Genes affected

TTN (HGNC:12403): (titin) This gene encodes a large abundant protein of striated muscle. The product of this gene is divided into two regions, a N-terminal I-band and a C-terminal A-band. The I-band, which is the elastic part of the molecule, contains two regions of tandem immunoglobulin domains on either side of a PEVK region that is rich in proline, glutamate, valine and lysine. The A-band, which is thought to act as a protein-ruler, contains a mixture of immunoglobulin and fibronectin repeats, and possesses kinase activity. An N-terminal Z-disc region and a C-terminal M-line region bind to the Z-line and M-line of the sarcomere, respectively, so that a single titin molecule spans half the length of a sarcomere. Titin also contains binding sites for muscle associated proteins so it serves as an adhesion template for the assembly of contractile machinery in muscle cells. It has also been identified as a structural protein for chromosomes. Alternative splicing of this gene results in multiple transcript variants. Considerable variability exists in the I-band, the M-line and the Z-disc regions of titin. Variability in the I-band region contributes to the differences in elasticity of different titin isoforms and, therefore, to the differences in elasticity of different muscle types. Mutations in this gene are associated with familial hypertrophic cardiomyopathy 9, and autoantibodies to titin are produced in patients with the autoimmune disease scleroderma. [provided by RefSeq, Feb 2012]

TTN-AS1 (HGNC:44124): (TTN antisense RNA 1) This gene encodes a non-coding RNA transcribed from the opposite strand to the titin gene. [provided by RefSeq, Aug 2016]

ACMG classification

Our verdict: Benign. The variant received -20 ACMG points.

• BP4: Computational evidence support a benign effect (MetaRNN=0.0015726686).
• BP6: Variant 2-178536168-C-T is Benign according to our data. Variant chr2-178536168-C-T is described in ClinVar as Benign/Likely_benign. ClinVar VariationId is 47629.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.137 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001267550.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TTN	NM_001267550.2	MANE Select	c.100579G>A	p.Val33527Ile	missense	Exon 357 of 363	NP_001254479.2	Q8WZ42-12
	TTN	NM_001256850.1		c.95656G>A	p.Val31886Ile	missense	Exon 307 of 313	NP_001243779.1	Q8WZ42-1
	TTN	NM_133378.4		c.92875G>A	p.Val30959Ile	missense	Exon 306 of 312	NP_596869.4	Q8WZ42-11

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TTN	ENST00000589042.5	TSL:5 MANE Select	c.100579G>A	p.Val33527Ile	missense	Exon 357 of 363	ENSP00000467141.1	Q8WZ42-12
	TTN	ENST00000446966.2	TSL:1	c.100423G>A	p.Val33475Ile	missense	Exon 355 of 361	ENSP00000408004.2	A0A1B0GXE3
	TTN	ENST00000436599.2	TSL:1	c.100303G>A	p.Val33435Ile	missense	Exon 355 of 361	ENSP00000405517.2	A0A0C4DG59

Frequencies

GnomAD3 genomes AF: 0.0379 AC: 5770 AN: 152050 Hom.: 194 Cov.: 33

Gnomad AFR AF: 0.0701

Gnomad AMI AF: 0.00439

Gnomad AMR AF: 0.0378

Gnomad ASJ AF: 0.0283

Gnomad EAS AF: 0.146

Gnomad SAS AF: 0.0124

Gnomad FIN AF: 0.00189

Gnomad MID AF: 0.0506

Gnomad NFE AF: 0.0180

Gnomad OTH AF: 0.0531

GnomAD2 exomes AF: 0.0317 AC: 7860 AN: 247972 AF XY: 0.0303

Gnomad AFR exome AF: 0.0698

Gnomad AMR exome AF: 0.0299

Gnomad ASJ exome AF: 0.0256

Gnomad EAS exome AF: 0.156

Gnomad FIN exome AF: 0.00339

Gnomad NFE exome AF: 0.0180

Gnomad OTH exome AF: 0.0319

GnomAD4 exome AF: 0.0240 AC: 35112 AN: 1461244 Hom.: 950 Cov.: 33 AF XY: 0.0234 AC XY: 17045 AN XY: 726868

African (AFR) AF: 0.0703 AC: 2352 AN: 33466

American (AMR) AF: 0.0316 AC: 1412 AN: 44656

Ashkenazi Jewish (ASJ) AF: 0.0253 AC: 662 AN: 26128

East Asian (EAS) AF: 0.164 AC: 6493 AN: 39670

South Asian (SAS) AF: 0.0136 AC: 1175 AN: 86242

European-Finnish (FIN) AF: 0.00313 AC: 167 AN: 53380

Middle Eastern (MID) AF: 0.0803 AC: 463 AN: 5764

European-Non Finnish (NFE) AF: 0.0185 AC: 20576 AN: 1111594

Other (OTH) AF: 0.0300 AC: 1812 AN: 60344

GnomAD4 genome AF: 0.0380 AC: 5778 AN: 152168 Hom.: 193 Cov.: 33 AF XY: 0.0372 AC XY: 2771 AN XY: 74406

African (AFR) AF: 0.0702 AC: 2914 AN: 41514

American (AMR) AF: 0.0378 AC: 577 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.0283 AC: 98 AN: 3464

East Asian (EAS) AF: 0.145 AC: 751 AN: 5164

South Asian (SAS) AF: 0.0127 AC: 61 AN: 4818

European-Finnish (FIN) AF: 0.00189 AC: 20 AN: 10610

Middle Eastern (MID) AF: 0.0544 AC: 16 AN: 294

European-Non Finnish (NFE) AF: 0.0180 AC: 1227 AN: 68004

Other (OTH) AF: 0.0520 AC: 110 AN: 2114

Alfa AF: 0.0278 Hom.: 414

Bravo AF: 0.0424

TwinsUK AF: 0.0178 AC: 66

ALSPAC AF: 0.0179 AC: 69

ESP6500AA AF: 0.0651 AC: 247

ESP6500EA AF: 0.0174 AC: 143

ExAC AF: 0.0309 AC: 3731

Asia WGS AF: 0.0600 AC: 209 AN: 3478

EpiCase AF: 0.0230

EpiControl AF: 0.0251

ClinVar

ClinVar submissions

Significance: Benign/Likely benign

Revision: criteria provided, multiple submitters, no conflicts

Pathogenic	VUS	Benign	Condition
-	-	8	not specified (8)
-	-	2	Autosomal recessive limb-girdle muscular dystrophy type 2J (2)
-	-	2	Early-onset myopathy with fatal cardiomyopathy (2)
-	-	2	Myopathy, myofibrillar, 9, with early respiratory failure (2)
-	-	2	not provided (2)
-	-	2	Tibial muscular dystrophy (2)
-	-	1	Autosomal recessive limb-girdle muscular dystrophy type 2J;C1858763:Dilated cardiomyopathy 1G (1)
-	-	1	Cardiovascular phenotype (1)
-	-	1	Dilated cardiomyopathy 1G (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.073
BayesDel_addAF	Benign	-0.51	T
BayesDel_noAF	Benign	-0.35
CADD	Benign	20
DANN	Benign	0.87
Eigen	Uncertain	0.21
Eigen_PC	Uncertain	0.37
FATHMM_MKL	Uncertain	0.96	D
LIST_S2	Uncertain	0.90	D
MetaRNN	Benign	0.0016	T
MetaSVM	Benign	-0.98	T
MutationAssessor	Benign	0.21	N
PhyloP100		4.8
PrimateAI	Uncertain	0.63	T
PROVEAN	Benign	-0.50	N
REVEL	Benign	0.21
Sift	Benign	0.24	T
Polyphen		0.77	P
Vest4		0.19
MPC		0.084
ClinPred		0.011	T
GERP RS		5.8
Mutation Taster		=94/6	polymorphism (auto)

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

Other links and lift over

dbSNP: rs2278196; hg19: chr2-179400895; COSMIC: COSV60452995; COSMIC: COSV60452995;