rs16866531

Variant names:

• chr2-178778905-T-C
• rs16866531
• NM_001267550.2:c.4177A>G

Your query was ambiguous. Multiple possible variants found:

• chr2-178778905-T-C
• chr2-178778905-T-G

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.4177A>G​(p.Ile1393Val) variant causes a missense change. The variant allele was found at a frequency of 0.00692 in 1,613,932 control chromosomes in the GnomAD database, including 694 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/18 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).

• Frequency:
  • Genomes: 𝑓 0.036 (335 hom., cov: 33)
  • Exomes 𝑓: 0.0039 (359 hom.)
• Consequence: TTN NM_001267550.2 missense
• Clinical Significance: Benign/Likely benign criteria provided, multiple submitters, no conflicts B:25
• Conservation: PhyloP100: 3.83
• Publications: 11 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]

LOC101927055 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (MetaRNN=0.0012234747).
• BP6: Variant 2-178778905-T-C is Benign according to our data. Variant chr2-178778905-T-C is described in ClinVar as Benign/Likely_benign. ClinVar VariationId is 47032.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.122 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TTN	NM_001267550.2	MANE Select	c.4177A>G	p.Ile1393Val	missense	Exon 24 of 363	NP_001254479.2
	TTN	NM_001256850.1		c.4177A>G	p.Ile1393Val	missense	Exon 24 of 313	NP_001243779.1
	TTN	NM_133378.4		c.4177A>G	p.Ile1393Val	missense	Exon 24 of 312	NP_596869.4

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TTN	ENST00000589042.5	TSL:5 MANE Select	c.4177A>G	p.Ile1393Val	missense	Exon 24 of 363	ENSP00000467141.1
	TTN	ENST00000446966.2	TSL:1	c.4177A>G	p.Ile1393Val	missense	Exon 24 of 361	ENSP00000408004.2
	TTN	ENST00000436599.2	TSL:1	c.3901A>G	p.Ile1301Val	missense	Exon 22 of 361	ENSP00000405517.2

Frequencies

GnomAD3 genomes AF: 0.0359 AC: 5457 AN: 152182 Hom.: 333 Cov.: 33

Gnomad AFR AF: 0.125

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0126

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.000207

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.0127

Gnomad NFE AF: 0.000426

Gnomad OTH AF: 0.0239

GnomAD2 exomes AF: 0.00972 AC: 2438 AN: 250890 AF XY: 0.00689

Gnomad AFR exome AF: 0.132

Gnomad AMR exome AF: 0.00616

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.00

Gnomad FIN exome AF: 0.0000462

Gnomad NFE exome AF: 0.000326

Gnomad OTH exome AF: 0.00491

GnomAD4 exome AF: 0.00389 AC: 5692 AN: 1461632 Hom.: 359 Cov.: 30 AF XY: 0.00328 AC XY: 2382 AN XY: 727124

African (AFR) AF: 0.138 AC: 4612 AN: 33460

American (AMR) AF: 0.00707 AC: 316 AN: 44718

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 26134

East Asian (EAS) AF: 0.00 AC: 0 AN: 39654

South Asian (SAS) AF: 0.000336 AC: 29 AN: 86256

European-Finnish (FIN) AF: 0.0000562 AC: 3 AN: 53398

Middle Eastern (MID) AF: 0.00520 AC: 30 AN: 5764

European-Non Finnish (NFE) AF: 0.000172 AC: 191 AN: 1111870

Other (OTH) AF: 0.00846 AC: 511 AN: 60378

GnomAD4 genome AF: 0.0360 AC: 5478 AN: 152300 Hom.: 335 Cov.: 33 AF XY: 0.0354 AC XY: 2635 AN XY: 74486

African (AFR) AF: 0.125 AC: 5203 AN: 41558

American (AMR) AF: 0.0126 AC: 192 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3468

East Asian (EAS) AF: 0.00 AC: 0 AN: 5186

South Asian (SAS) AF: 0.00 AC: 0 AN: 4830

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 10628

Middle Eastern (MID) AF: 0.0136 AC: 4 AN: 294

European-Non Finnish (NFE) AF: 0.000426 AC: 29 AN: 68020

Other (OTH) AF: 0.0237 AC: 50 AN: 2114

Alfa AF: 0.0118 Hom.: 389

Bravo AF: 0.0424

ESP6500AA AF: 0.131 AC: 579

ESP6500EA AF: 0.000349 AC: 3

ExAC AF: 0.0121 AC: 1472

Asia WGS AF: 0.00751 AC: 27 AN: 3478

EpiCase AF: 0.000273

EpiControl AF: 0.000474

ClinVar

ClinVar submissions as Germline

Significance: Benign/Likely benign

Revision: criteria provided, multiple submitters, no conflicts

Pathogenic	VUS	Benign	Condition
-	-	11	not specified (11)
-	-	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	Cardiomyopathy (1)
-	-	1	Cardiovascular phenotype (1)
-	-	1	Dilated cardiomyopathy 1G (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.088
BayesDel_addAF	Benign	-0.61	T
BayesDel_noAF	Benign	-0.54
CADD	Benign	20
DANN	Benign	0.94
Eigen	Benign	-0.058
Eigen_PC	Benign	0.14
FATHMM_MKL	Uncertain	0.95	D
LIST_S2	Benign	0.77	T
MetaRNN	Benign	0.0012	T
MetaSVM	Benign	-1.1	T
PhyloP100		3.8
PrimateAI	Benign	0.48	T
PROVEAN	Benign	-0.29	N
REVEL	Benign	0.095
Sift	Benign	1.0	T
Sift4G	Benign	0.15	T
Polyphen		0.0010	B
Vest4		0.042
MPC		0.071
ClinPred		0.011	T
GERP RS		4.7
Mutation Taster		=95/5	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: rs16866531; hg19: chr2-179643632;