rs143473183

Variant summary

Our verdict is Benign. Variant got -7 ACMG points: 2P and 9B. PM2BP4_StrongBP6BS1

The NM_001164508.2(NEB):​c.9181A>T​(p.Met3061Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00027 in 1,613,996 control chromosomes in the GnomAD database, including 1 homozygotes. 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 Conflicting classifications of pathogenicity (no stars).

Frequency

Genomes: 𝑓 0.0015 ( 1 hom., cov: 32)
Exomes 𝑓: 0.00014 ( 0 hom. )

Consequence

NEB
NM_001164508.2 missense

Scores

2
14

Clinical Significance

Conflicting classifications of pathogenicity criteria provided, conflicting classifications U:3B:3

Conservation

PhyloP100: -0.0960
Variant links:
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]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -7 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.013075799).
BP6
Variant 2-151633887-T-A is Benign according to our data. Variant chr2-151633887-T-A is described in ClinVar as [Conflicting_classifications_of_pathogenicity]. Clinvar id is 450097.We mark this variant Likely_benign, oryginal submissions are: {Uncertain_significance=2, Likely_benign=2}.
BS1
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.00149 (227/152292) while in subpopulation AFR AF= 0.0052 (216/41562). AF 95% confidence interval is 0.00463. There are 1 homozygotes in gnomad4. There are 121 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
NEBNM_001164507.2 linkuse as main transcriptc.9181A>T p.Met3061Leu missense_variant 65/182 ENST00000427231.7 NP_001157979.2
NEBNM_001164508.2 linkuse as main transcriptc.9181A>T p.Met3061Leu missense_variant 65/182 ENST00000397345.8 NP_001157980.2

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
NEBENST00000397345.8 linkuse as main transcriptc.9181A>T p.Met3061Leu missense_variant 65/1825 NM_001164508.2 ENSP00000380505 P5P20929-2
NEBENST00000427231.7 linkuse as main transcriptc.9181A>T p.Met3061Leu missense_variant 65/1825 NM_001164507.2 ENSP00000416578 A2P20929-3
NEBENST00000409198.5 linkuse as main transcriptc.8854-2709A>T intron_variant 5 ENSP00000386259 P20929-4

Frequencies

GnomAD3 genomes
AF:
0.00143
AC:
217
AN:
152174
Hom.:
0
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.00495
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.000524
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.000415
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.00
Gnomad OTH
AF:
0.000956
GnomAD3 exomes
AF:
0.000341
AC:
85
AN:
249256
Hom.:
0
AF XY:
0.000266
AC XY:
36
AN XY:
135218
show subpopulations
Gnomad AFR exome
AF:
0.00471
Gnomad AMR exome
AF:
0.000145
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.0000980
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.0000265
Gnomad OTH exome
AF:
0.000165
GnomAD4 exome
AF:
0.000143
AC:
209
AN:
1461704
Hom.:
0
Cov.:
115
AF XY:
0.000132
AC XY:
96
AN XY:
727134
show subpopulations
Gnomad4 AFR exome
AF:
0.00493
Gnomad4 AMR exome
AF:
0.000246
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.0000252
Gnomad4 SAS exome
AF:
0.0000464
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.00000270
Gnomad4 OTH exome
AF:
0.000398
GnomAD4 genome
AF:
0.00149
AC:
227
AN:
152292
Hom.:
1
Cov.:
32
AF XY:
0.00162
AC XY:
121
AN XY:
74474
show subpopulations
Gnomad4 AFR
AF:
0.00520
Gnomad4 AMR
AF:
0.000523
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.000207
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.00
Gnomad4 OTH
AF:
0.000946
Alfa
AF:
0.000812
Hom.:
0
Bravo
AF:
0.00145
ESP6500AA
AF:
0.00361
AC:
5
ESP6500EA
AF:
0.00
AC:
0
ExAC
AF:
0.000389
AC:
47
Asia WGS
AF:
0.00115
AC:
4
AN:
3478
EpiCase
AF:
0.0000545
EpiControl
AF:
0.00

ClinVar

Significance: Conflicting classifications of pathogenicity
Submissions summary: Uncertain:3Benign:3
Revision: criteria provided, conflicting classifications
LINK: link

Submissions by phenotype

not provided Uncertain:2Benign:1
Uncertain significance, criteria provided, single submitterclinical testingRevvity Omics, RevvityAug 07, 2019- -
Likely benign, criteria provided, single submitterclinical testingGeneDxMay 21, 2018- -
Uncertain significance, criteria provided, single submitterclinical testingAthena DiagnosticsJul 20, 2018- -
Nemaline myopathy 2 Uncertain:1Benign:1
Likely benign, criteria provided, single submitterclinical testingLabcorp Genetics (formerly Invitae), LabcorpJan 24, 2024- -
Uncertain significance, no assertion criteria providedclinical testingNatera, Inc.Jan 17, 2020- -
NEB-related disorder Benign:1
Likely benign, no assertion criteria providedclinical testingPreventionGenetics, part of Exact SciencesJun 08, 2020This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_addAF
Benign
-0.44
T
BayesDel_noAF
Benign
-0.41
CADD
Benign
15
DANN
Benign
0.93
DEOGEN2
Benign
0.023
.;T;.;.;.
Eigen
Benign
0.12
Eigen_PC
Benign
0.22
FATHMM_MKL
Uncertain
0.77
D
LIST_S2
Benign
0.80
T;T;T;.;.
M_CAP
Benign
0.017
T
MetaRNN
Benign
0.013
T;T;T;T;T
MetaSVM
Benign
-1.0
T
MutationTaster
Benign
1.0
D;D;N;N
PROVEAN
Benign
-0.98
N;.;N;.;.
REVEL
Benign
0.087
Sift
Benign
0.090
T;.;T;.;.
Sift4G
Uncertain
0.019
D;D;D;D;D
Vest4
0.29
MutPred
0.48
Loss of catalytic residue at M3061 (P = 0.0109);Loss of catalytic residue at M3061 (P = 0.0109);Loss of catalytic residue at M3061 (P = 0.0109);Loss of catalytic residue at M3061 (P = 0.0109);Loss of catalytic residue at M3061 (P = 0.0109);
MVP
0.36
MPC
0.050
ClinPred
0.041
T
GERP RS
6.0
gMVP
0.019

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

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs143473183; hg19: chr2-152490401; API