rs56214710

Variant names:

• chr2-178564277-G-A
• rs56214710
• NM_001267550.2:c.81855C>T

Variant summary

Our verdict is Benign. The variant received -19 ACMG points: 0P and 19B. BP4_Moderate BP6_Very_Strong BP7 BA1

The NM_001267550.2(TTN):​c.81855C>T​(p.Ile27285Ile) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0227 in 1,613,266 control chromosomes in the GnomAD database, including 520 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).

• Frequency:
  • Genomes: 𝑓 0.020 (50 hom., cov: 33)
  • Exomes 𝑓: 0.023 (470 hom.)
• Consequence: TTN NM_001267550.2 synonymous
• Clinical Significance: Benign/Likely benign criteria provided, multiple submitters, no conflicts B:25
• Conservation: PhyloP100: 1.67
• Publications: 8 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 -19 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.33).
• BP6: Variant 2-178564277-G-A is Benign according to our data. Variant chr2-178564277-G-A is described in ClinVar as Benign/Likely_benign. ClinVar VariationId is 47402.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BP7: Synonymous conserved (PhyloP=1.67 with no splicing effect.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.0542 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.81855C>T	p.Ile27285Ile	synonymous	Exon 326 of 363	NP_001254479.2	Q8WZ42-12
	TTN	NM_001256850.1		c.76932C>T	p.Ile25644Ile	synonymous	Exon 276 of 313	NP_001243779.1	Q8WZ42-1
	TTN	NM_133378.4		c.74151C>T	p.Ile24717Ile	synonymous	Exon 275 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.81855C>T	p.Ile27285Ile	synonymous	Exon 326 of 363	ENSP00000467141.1	Q8WZ42-12
	TTN	ENST00000446966.2	TSL:1	c.81699C>T	p.Ile27233Ile	synonymous	Exon 324 of 361	ENSP00000408004.2	A0A1B0GXE3
	TTN	ENST00000436599.2	TSL:1	c.81579C>T	p.Ile27193Ile	synonymous	Exon 324 of 361	ENSP00000405517.2	A0A0C4DG59

Frequencies

GnomAD3 genomes AF: 0.0201 AC: 3056 AN: 152080 Hom.: 50 Cov.: 33

Gnomad AFR AF: 0.00449

Gnomad AMI AF: 0.0307

Gnomad AMR AF: 0.0215

Gnomad ASJ AF: 0.0190

Gnomad EAS AF: 0.0596

Gnomad SAS AF: 0.00808

Gnomad FIN AF: 0.0445

Gnomad MID AF: 0.00633

Gnomad NFE AF: 0.0233

Gnomad OTH AF: 0.0196

GnomAD2 exomes AF: 0.0257 AC: 6383 AN: 248028 AF XY: 0.0243

Gnomad AFR exome AF: 0.00485

Gnomad AMR exome AF: 0.0337

Gnomad ASJ exome AF: 0.0141

Gnomad EAS exome AF: 0.0592

Gnomad FIN exome AF: 0.0472

Gnomad NFE exome AF: 0.0231

Gnomad OTH exome AF: 0.0260

GnomAD4 exome AF: 0.0230 AC: 33615 AN: 1461068 Hom.: 470 Cov.: 37 AF XY: 0.0226 AC XY: 16436 AN XY: 726842

African (AFR) AF: 0.00403 AC: 135 AN: 33468

American (AMR) AF: 0.0319 AC: 1426 AN: 44718

Ashkenazi Jewish (ASJ) AF: 0.0143 AC: 374 AN: 26126

East Asian (EAS) AF: 0.0619 AC: 2455 AN: 39688

South Asian (SAS) AF: 0.00663 AC: 572 AN: 86258

European-Finnish (FIN) AF: 0.0482 AC: 2551 AN: 52918

Middle Eastern (MID) AF: 0.0101 AC: 58 AN: 5766

European-Non Finnish (NFE) AF: 0.0222 AC: 24727 AN: 1111760

Other (OTH) AF: 0.0218 AC: 1317 AN: 60366

GnomAD4 genome AF: 0.0201 AC: 3053 AN: 152198 Hom.: 50 Cov.: 33 AF XY: 0.0205 AC XY: 1522 AN XY: 74390

African (AFR) AF: 0.00448 AC: 186 AN: 41556

American (AMR) AF: 0.0215 AC: 329 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.0190 AC: 66 AN: 3470

East Asian (EAS) AF: 0.0597 AC: 308 AN: 5158

South Asian (SAS) AF: 0.00747 AC: 36 AN: 4820

European-Finnish (FIN) AF: 0.0445 AC: 471 AN: 10584

Middle Eastern (MID) AF: 0.00680 AC: 2 AN: 294

European-Non Finnish (NFE) AF: 0.0233 AC: 1586 AN: 67998

Other (OTH) AF: 0.0194 AC: 41 AN: 2112

Alfa AF: 0.0230 Hom.: 105

Bravo AF: 0.0184

Asia WGS AF: 0.0280 AC: 97 AN: 3476

EpiCase AF: 0.0200

EpiControl AF: 0.0216

ClinVar

ClinVar submissions

Significance: Benign/Likely benign

Revision: criteria provided, multiple submitters, no conflicts

Pathogenic	VUS	Benign	Condition
-	-	11	not specified (11)
-	-	3	not provided (3)
-	-	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	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
BayesDel_noAF	Benign	-0.33
CADD	Benign	0.16
DANN	Benign	0.84
PhyloP100		1.7
Mutation Taster		=98/2	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: rs56214710; hg19: chr2-179429004; COSMIC: COSV60085078;