rs117018177

Variant summary

Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BS1BS2

The NM_001164508.2(NEB):​c.11004G>A​(p.Thr3668Thr) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00194 in 1,613,946 control chromosomes in the GnomAD database, including 59 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.0026 ( 9 hom., cov: 32)
Exomes 𝑓: 0.0019 ( 50 hom. )

Consequence

NEB
NM_001164508.2 synonymous

Scores

2

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:8

Conservation

PhyloP100: -3.96
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 -21 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.71).
BP6
Variant 2-151618347-C-T is Benign according to our data. Variant chr2-151618347-C-T is described in ClinVar as [Benign]. Clinvar id is 198646.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BP7
Synonymous conserved (PhyloP=-3.96 with no splicing effect.
BS1
Variant frequency is greater than expected in population eas. gnomad4 allele frequency = 0.00261 (397/152282) while in subpopulation EAS AF= 0.0531 (275/5178). AF 95% confidence interval is 0.048. There are 9 homozygotes in gnomad4. There are 222 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
High Homozygotes in GnomAd4 at 9 AR gene

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
NEBNM_001164507.2 linkuse as main transcriptc.11004G>A p.Thr3668Thr synonymous_variant 74/182 ENST00000427231.7 NP_001157979.2
NEBNM_001164508.2 linkuse as main transcriptc.11004G>A p.Thr3668Thr synonymous_variant 74/182 ENST00000397345.8 NP_001157980.2

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
NEBENST00000397345.8 linkuse as main transcriptc.11004G>A p.Thr3668Thr synonymous_variant 74/1825 NM_001164508.2 ENSP00000380505.3 P20929-2
NEBENST00000427231.7 linkuse as main transcriptc.11004G>A p.Thr3668Thr synonymous_variant 74/1825 NM_001164507.2 ENSP00000416578.2 P20929-3
NEBENST00000409198.5 linkuse as main transcriptc.10275G>A p.Thr3425Thr synonymous_variant 71/1505 ENSP00000386259.1 P20929-4

Frequencies

GnomAD3 genomes
AF:
0.00264
AC:
401
AN:
152164
Hom.:
9
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.000483
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00419
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.0539
Gnomad SAS
AF:
0.00456
Gnomad FIN
AF:
0.000377
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.000103
Gnomad OTH
AF:
0.00191
GnomAD3 exomes
AF:
0.00611
AC:
1522
AN:
248944
Hom.:
30
AF XY:
0.00564
AC XY:
762
AN XY:
135024
show subpopulations
Gnomad AFR exome
AF:
0.000258
Gnomad AMR exome
AF:
0.0111
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.0548
Gnomad SAS exome
AF:
0.00376
Gnomad FIN exome
AF:
0.000278
Gnomad NFE exome
AF:
0.0000887
Gnomad OTH exome
AF:
0.00331
GnomAD4 exome
AF:
0.00187
AC:
2733
AN:
1461664
Hom.:
50
Cov.:
31
AF XY:
0.00184
AC XY:
1341
AN XY:
727120
show subpopulations
Gnomad4 AFR exome
AF:
0.000209
Gnomad4 AMR exome
AF:
0.0102
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.0407
Gnomad4 SAS exome
AF:
0.00368
Gnomad4 FIN exome
AF:
0.000356
Gnomad4 NFE exome
AF:
0.0000630
Gnomad4 OTH exome
AF:
0.00411
GnomAD4 genome
AF:
0.00261
AC:
397
AN:
152282
Hom.:
9
Cov.:
32
AF XY:
0.00298
AC XY:
222
AN XY:
74456
show subpopulations
Gnomad4 AFR
AF:
0.000481
Gnomad4 AMR
AF:
0.00418
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.0531
Gnomad4 SAS
AF:
0.00456
Gnomad4 FIN
AF:
0.000377
Gnomad4 NFE
AF:
0.000103
Gnomad4 OTH
AF:
0.00237
Alfa
AF:
0.000767
Hom.:
1
Bravo
AF:
0.00351
Asia WGS
AF:
0.0150
AC:
53
AN:
3478
EpiCase
AF:
0.000273
EpiControl
AF:
0.00

ClinVar

Significance: Benign
Submissions summary: Benign:8
Revision: criteria provided, multiple submitters, no conflicts
LINK: link

Submissions by phenotype

not specified Benign:3
Benign, criteria provided, single submitterclinical testingEurofins Ntd Llc (ga)Feb 13, 2015- -
Benign, criteria provided, single submitterclinical testingGeneDxDec 07, 2016This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. -
Benign, criteria provided, single submitterclinical testingPreventionGenetics, part of Exact Sciences-- -
Nemaline myopathy 2 Benign:3
Benign, criteria provided, single submitterclinical testingLabcorp Genetics (formerly Invitae), LabcorpFeb 01, 2024- -
Benign, criteria provided, single submitterclinical testingIllumina Laboratory Services, IlluminaJan 12, 2018This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. -
Benign, no assertion criteria providedclinical testingNatera, Inc.Sep 16, 2020- -
not provided Benign:2
Benign, criteria provided, single submitterclinical testingWomen's Health and Genetics/Laboratory Corporation of America, LabCorpApr 24, 2017Variant summary: The NEB c.11004G>A (p.Thr3668Thr) variant involves the alteration of a non-conserved nucleotide, resulting in a synonymous change and 5/5 splice prediction tools predict no significant impact on normal splicing. ESE finder predicts that this variant may affect ESE binding. However, these predictions have yet to be confirmed by functional studies. This variant was found in 687/120688 control chromosomes (15 homozygotes) at a frequency of 0.0056924, which is approximately 2 times the estimated maximal expected allele frequency of a pathogenic NEB variant (0.0035355), suggesting this variant is likely a benign polymorphism. In addition, multiple clinical diagnostic laboratories/reputable databases classified this variant as "likely benign/benign." Therefore, the variant of interest has been classified as Benign. -
Benign, criteria provided, single submitterclinical testingAthena DiagnosticsJun 27, 2019- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.71
CADD
Benign
0.29
DANN
Benign
0.35

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: rs117018177; hg19: chr2-152474861; COSMIC: COSV51453830; COSMIC: COSV51453830; API