chr2-151582622-A-C

Position:

• chr2-151582622-A-C

Variant summary

Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_Strong BP6_Moderate

The NM_001164507.2(NEB):​c.16021T>G​(p.Leu5341Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. 12/17 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★). Synonymous variant affecting the same amino acid position (i.e. L5341L) has been classified as Benign.

• Frequency: Genomes: not found (cov: 0)
• Consequence: NEB NM_001164507.2 missense
• Clinical Significance: Likely benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.629

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 -6 ACMG points.

• BP4: Computational evidence support a benign effect (MetaRNN=0.05163741).
• BP6: Variant 2-151582622-A-C is Benign according to our data. Variant chr2-151582622-A-C is described in ClinVar as [Likely_benign]. Clinvar id is 1213020.Status of the report is criteria_provided_single_submitter, 1 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
NEB	NM_001164507.2	c.16021T>G	p.Leu5341Val	missense_variant	102/182	ENST00000427231.7
NEB	NM_001164508.2	c.16021T>G	p.Leu5341Val	missense_variant	102/182	ENST00000397345.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
NEB	ENST00000397345.8	c.16021T>G	p.Leu5341Val	missense_variant	102/182	5	NM_001164508.2	P5
NEB	ENST00000427231.7	c.16021T>G	p.Leu5341Val	missense_variant	102/182	5	NM_001164507.2	A2
NEB	ENST00000413693.5	c.211T>G	p.Leu71Val	missense_variant	2/74	5
NEB	ENST00000409198.5	c.11602-6268T>G		intron_variant		5

Frequencies

GnomAD3 genomes Cov.: 0

GnomAD4 exome Cov.: 0

GnomAD4 genome Cov.: 0

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Likely benign, criteria provided, single submitter

clinical testing

GeneDx

May 31, 2019

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_addAF	Benign	-0.37	T
BayesDel_noAF	Benign	-0.76
CADD	Benign	18
DANN	Benign	0.83
DEOGEN2	Benign	0.0022	.;T;.;T;.;.
Eigen	Benign	-0.76
Eigen_PC	Benign	-0.52
FATHMM_MKL	Benign	0.42	N
LIST_S2	Benign	0.33	T;T;T;T;.;.
M_CAP	Benign	0.027	D
MetaRNN	Benign	0.052	T;T;T;T;T;T
MetaSVM	Benign	-0.97	T
MutationTaster	Benign	1.0	D;D;N;N
PROVEAN	Benign	-0.070	N;.;N;N;.;.
REVEL	Benign	0.13
Sift	Benign	1.0	T;.;T;T;.;.
Sift4G	Benign	0.23	T;T;T;T;T;T
Vest4		0.30
MutPred		0.41		Loss of catalytic residue at L5341 (P = 0.0696);Loss of catalytic residue at L5341 (P = 0.0696);Loss of catalytic residue at L5341 (P = 0.0696);.;Loss of catalytic residue at L5341 (P = 0.0696);Loss of catalytic residue at L5341 (P = 0.0696);
MVP		0.17
MPC		0.29
ClinPred		0.25	T
GERP RS		4.3
gMVP		0.0012

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

No publications associated with this variant yet.

Other links and lift over

hg19: chr2-152439136;