chr2-178685342-T-C

Variant names:

• chr2-178685342-T-C
• rs16866434
• NM_001267550.2:c.32393-12A>G

Variant summary

Our verdict is Benign. The variant received -18 ACMG points: 0P and 18B. BP4_Moderate BP6_Very_Strong BA1

The NM_001267550.2(TTN):​c.32393-12A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0131 in 1,544,738 control chromosomes in the GnomAD database, including 281 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).

• Frequency:
  • Genomes: 𝑓 0.028 (118 hom., cov: 32)
  • Exomes 𝑓: 0.011 (163 hom.)
• Consequence: TTN NM_001267550.2 intron
• Scores: Splicing: ADA: 0.0005552
• Clinical Significance: Benign/Likely benign criteria provided, multiple submitters, no conflicts B:20
• Conservation: PhyloP100: 1.33
• Publications: 5 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]

LOC124906100 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -18 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.25).
• BP6: Variant 2-178685342-T-C is Benign according to our data. Variant chr2-178685342-T-C is described in ClinVar as Benign/Likely_benign. ClinVar VariationId is 46866.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0666 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.32393-12A>G		intron	N/A	NP_001254479.2	Q8WZ42-12
	TTN	NM_001256850.1		c.31442-12A>G		intron	N/A	NP_001243779.1	Q8WZ42-1
	TTN	NM_133378.4		c.28661-12A>G		intron	N/A	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.32393-12A>G		intron	N/A	ENSP00000467141.1	Q8WZ42-12
	TTN	ENST00000446966.2	TSL:1	c.32393-12A>G		intron	N/A	ENSP00000408004.2	A0A1B0GXE3
	TTN	ENST00000436599.2	TSL:1	c.32117-12A>G		intron	N/A	ENSP00000405517.2	A0A0C4DG59

Frequencies

GnomAD3 genomes AF: 0.0277 AC: 4214 AN: 152178 Hom.: 119 Cov.: 32

Gnomad AFR AF: 0.0686

Gnomad AMI AF: 0.00548

Gnomad AMR AF: 0.0255

Gnomad ASJ AF: 0.00490

Gnomad EAS AF: 0.00769

Gnomad SAS AF: 0.0178

Gnomad FIN AF: 0.0178

Gnomad MID AF: 0.0253

Gnomad NFE AF: 0.00850

Gnomad OTH AF: 0.0292

GnomAD2 exomes AF: 0.0153 AC: 2327 AN: 152578 AF XY: 0.0152

Gnomad AFR exome AF: 0.0692

Gnomad AMR exome AF: 0.0131

Gnomad ASJ exome AF: 0.00463

Gnomad EAS exome AF: 0.00693

Gnomad FIN exome AF: 0.0183

Gnomad NFE exome AF: 0.00944

Gnomad OTH exome AF: 0.0144

GnomAD4 exome AF: 0.0115 AC: 15955 AN: 1392442 Hom.: 163 Cov.: 31 AF XY: 0.0116 AC XY: 7940 AN XY: 686582

African (AFR) AF: 0.0687 AC: 2146 AN: 31244

American (AMR) AF: 0.0139 AC: 486 AN: 35056

Ashkenazi Jewish (ASJ) AF: 0.00483 AC: 121 AN: 25048

East Asian (EAS) AF: 0.00330 AC: 118 AN: 35804

South Asian (SAS) AF: 0.0197 AC: 1522 AN: 77178

European-Finnish (FIN) AF: 0.0158 AC: 778 AN: 49266

Middle Eastern (MID) AF: 0.0237 AC: 132 AN: 5580

European-Non Finnish (NFE) AF: 0.00904 AC: 9719 AN: 1075514

Other (OTH) AF: 0.0162 AC: 933 AN: 57752

GnomAD4 genome AF: 0.0277 AC: 4223 AN: 152296 Hom.: 118 Cov.: 32 AF XY: 0.0281 AC XY: 2089 AN XY: 74468

African (AFR) AF: 0.0687 AC: 2853 AN: 41550

American (AMR) AF: 0.0254 AC: 389 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.00490 AC: 17 AN: 3470

East Asian (EAS) AF: 0.00751 AC: 39 AN: 5192

South Asian (SAS) AF: 0.0174 AC: 84 AN: 4830

European-Finnish (FIN) AF: 0.0178 AC: 189 AN: 10606

Middle Eastern (MID) AF: 0.0272 AC: 8 AN: 294

European-Non Finnish (NFE) AF: 0.00850 AC: 578 AN: 68030

Other (OTH) AF: 0.0289 AC: 61 AN: 2114

Alfa AF: 0.0167 Hom.: 21

Bravo AF: 0.0294

Asia WGS AF: 0.0130 AC: 46 AN: 3470

ClinVar

ClinVar submissions

Significance: Benign/Likely benign

Revision: criteria provided, multiple submitters, no conflicts

Pathogenic	VUS	Benign	Condition
-	-	7	not specified (7)
-	-	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	Dilated cardiomyopathy 1G (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.25
CADD	Benign	19
DANN	Benign	0.82
PhyloP100		1.3
Mutation Taster		=98/2	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
dbscSNV1_ADA	Benign	0.00056
dbscSNV1_RF	Benign	0.17
SpliceAI score (max)		0.16		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: rs16866434; hg19: chr2-179550069;