2-151485796-G-A

Variant summary

Our verdict is Benign. Variant got -19 ACMG points: 0P and 19B. BP4_ModerateBP6_Very_StrongBP7BS1BS2

The NM_001164507.2(NEB):​c.25542C>T​(p.Thr8514=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00169 in 1,612,818 control chromosomes in the GnomAD database, including 41 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.0024 ( 9 hom., cov: 32)
Exomes 𝑓: 0.0016 ( 32 hom. )

Consequence

NEB
NM_001164507.2 synonymous

Scores

2

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:7

Conservation

PhyloP100: -1.22
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]
RIF1 (HGNC:23207): (replication timing regulatory factor 1) This gene encodes a protein that shares homology with the yeast teleomere binding protein, Rap1 interacting factor 1. This protein localizes to aberrant telomeres may be involved in DNA repair. Alternate splicing results in multiple transcript variants. [provided by RefSeq, Apr 2010]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -19 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.44).
BP6
Variant 2-151485796-G-A is Benign according to our data. Variant chr2-151485796-G-A is described in ClinVar as [Benign]. Clinvar id is 194578.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BP7
Synonymous conserved (PhyloP=-1.22 with no splicing effect.
BS1
Variant frequency is greater than expected in population eas. gnomad4 allele frequency = 0.00237 (361/152264) while in subpopulation EAS AF= 0.0457 (237/5182). AF 95% confidence interval is 0.041. There are 9 homozygotes in gnomad4. There are 186 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.25542C>T p.Thr8514= synonymous_variant 182/182 ENST00000427231.7 NP_001157979.2
NEBNM_001164508.2 linkuse as main transcriptc.25542C>T p.Thr8514= synonymous_variant 182/182 ENST00000397345.8 NP_001157980.2

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
NEBENST00000397345.8 linkuse as main transcriptc.25542C>T p.Thr8514= synonymous_variant 182/1825 NM_001164508.2 ENSP00000380505 P5P20929-2
NEBENST00000427231.7 linkuse as main transcriptc.25542C>T p.Thr8514= synonymous_variant 182/1825 NM_001164507.2 ENSP00000416578 A2P20929-3

Frequencies

GnomAD3 genomes
AF:
0.00239
AC:
364
AN:
152146
Hom.:
9
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.000531
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00380
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.0464
Gnomad SAS
AF:
0.00269
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.000323
Gnomad OTH
AF:
0.00383
GnomAD3 exomes
AF:
0.00543
AC:
1348
AN:
248224
Hom.:
24
AF XY:
0.00503
AC XY:
677
AN XY:
134546
show subpopulations
Gnomad AFR exome
AF:
0.000258
Gnomad AMR exome
AF:
0.0103
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.0484
Gnomad SAS exome
AF:
0.00190
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.000383
Gnomad OTH exome
AF:
0.00299
GnomAD4 exome
AF:
0.00161
AC:
2357
AN:
1460554
Hom.:
32
Cov.:
31
AF XY:
0.00154
AC XY:
1122
AN XY:
726380
show subpopulations
Gnomad4 AFR exome
AF:
0.000418
Gnomad4 AMR exome
AF:
0.00969
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.0311
Gnomad4 SAS exome
AF:
0.00190
Gnomad4 FIN exome
AF:
0.0000375
Gnomad4 NFE exome
AF:
0.000240
Gnomad4 OTH exome
AF:
0.00401
GnomAD4 genome
AF:
0.00237
AC:
361
AN:
152264
Hom.:
9
Cov.:
32
AF XY:
0.00250
AC XY:
186
AN XY:
74454
show subpopulations
Gnomad4 AFR
AF:
0.000529
Gnomad4 AMR
AF:
0.00379
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.0457
Gnomad4 SAS
AF:
0.00269
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.000323
Gnomad4 OTH
AF:
0.00426
Alfa
AF:
0.00113
Hom.:
1
Bravo
AF:
0.00321
Asia WGS
AF:
0.0170
AC:
59
AN:
3478
EpiCase
AF:
0.000657
EpiControl
AF:
0.000476

ClinVar

Significance: Benign
Submissions summary: Benign:7
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 testingGeneDxJul 08, 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-- -
not provided Benign:2
Benign, criteria provided, single submitterclinical testingWomen's Health and Genetics/Laboratory Corporation of America, LabCorpApr 24, 2017Variant summary: The c.25647C>T (p.Thr8549=) in NEB gene is a synonymous change that involves a non-conserved nucleotide. 5/5 programs in Alamut predict that this variant does not affect a normal splicing, however no functional studies supporting this notion were published at the time of evaluation. The variant is present in control population dataset of ExAC at a frequency of 0.0049 (593/120504 chrs tested), predominantly in individuals of East Asian descent (0.047; 403/8622chrs tested, including 12 homozygotes). These frequencies exceed the estimated maximal expected allele frequency of a pathogenic variant in NEB gene (0.0035). Lastly, multiple reputable databases/diagnostic centers classified the variant of interest as Benign. Taking together, the variant was classified as Benign. -
Benign, criteria provided, single submitterclinical testingAthena DiagnosticsJun 27, 2019- -
Nemaline myopathy 2 Benign:2
Benign, criteria provided, single submitterclinical testingLabcorp Genetics (formerly Invitae), LabcorpFeb 01, 2024- -
Benign, criteria provided, single submitterclinical testingIllumina Laboratory Services, IlluminaJan 13, 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. -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.44
CADD
Benign
1.9
DANN
Benign
0.82

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: rs3821324; hg19: chr2-152342310; COSMIC: COSV51426418; COSMIC: COSV51426418; API