2-151601912-T-G

Position:

• chr2-151601912-T-G

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 0P and 2B. BP4_Moderate

The NM_001164507.2(NEB):​c.13465A>C​(p.Ile4489Leu) variant causes a missense change. In-silico tool predicts a benign outcome for this variant. 11/17 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. I4489T) has been classified as Likely benign.

• Frequency: Genomes: not found (cov: 0)
• Consequence: NEB NM_001164507.2 missense
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1
• Conservation: PhyloP100: 6.72

Genes affected

NEB (HGNC:7720): (nebulin) This gene encodes nebulin, a giant protein component of the cytoskeletal matrix that coexists with the thick and thin filaments within the sarcomeres of skeletal muscle. In most vertebrates, nebulin accounts for 3 to 4% of the total myofibrillar protein. The encoded protein contains approximately 30-amino acid long modules that can be classified into 7 types and other repeated modules. Protein isoform sizes vary from 600 to 800 kD due to alternative splicing that is tissue-, species-,and developmental stage-specific. Of the 183 exons in the nebulin gene, at least 43 are alternatively spliced, although exons 143 and 144 are not found in the same transcript. Of the several thousand transcript variants predicted for nebulin, the RefSeq Project has decided to create three representative RefSeq records. Mutations in this gene are associated with recessive nemaline myopathy. [provided by RefSeq, Sep 2009]

ACMG classification

Verdict is Likely_benign. Variant got -2 ACMG points.

• BP4: Computational evidence support a benign effect (MetaRNN=0.24877241).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
NEB	NM_001164507.2	c.13465A>C	p.Ile4489Leu	missense_variant	88/182	ENST00000427231.7
NEB	NM_001164508.2	c.13465A>C	p.Ile4489Leu	missense_variant	88/182	ENST00000397345.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
NEB	ENST00000397345.8	c.13465A>C	p.Ile4489Leu	missense_variant	88/182	5	NM_001164508.2	P5
NEB	ENST00000427231.7	c.13465A>C	p.Ile4489Leu	missense_variant	88/182	5	NM_001164507.2	A2
NEB	ENST00000409198.5	c.11601+7897A>C		intron_variant		5

Frequencies

GnomAD3 genomes Cov.: 0

GnomAD4 exome Cov.: 0

GnomAD4 genome Cov.: 0

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:1

Revision: criteria provided, single submitter

Submissions by phenotype

Nemaline myopathy 2 Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

Invitae

Jun 30, 2017

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_addAF	Benign	-0.11	T
BayesDel_noAF	Benign	-0.39
CADD	Benign	22
DANN	Benign	0.92
DEOGEN2	Benign	0.011	.;T;.;.;.
Eigen	Benign	-0.083
Eigen_PC	Benign	-0.093
FATHMM_MKL	Uncertain	0.94	D
LIST_S2	Benign	0.67	T;T;T;.;.
M_CAP	Benign	0.014	T
MetaRNN	Benign	0.25	T;T;T;T;T
MetaSVM	Benign	-1.1	T
MutationTaster	Benign	0.90	D;D;D;D
PROVEAN	Benign	-0.18	N;.;N;.;.
REVEL	Benign	0.10
Sift	Benign	0.043	D;.;D;.;.
Sift4G	Uncertain	0.014	D;D;D;D;D
Vest4		0.45
MutPred		0.52		Loss of ubiquitination at K4484 (P = 0.1231);Loss of ubiquitination at K4484 (P = 0.1231);Loss of ubiquitination at K4484 (P = 0.1231);Loss of ubiquitination at K4484 (P = 0.1231);Loss of ubiquitination at K4484 (P = 0.1231);
MVP		0.46
MPC		0.10
ClinPred		0.46	T
GERP RS		2.9
gMVP		0.0026

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

Other links and lift over

dbSNP: rs1553865611; hg19: chr2-152458426;