2-151501528-T-C

Variant names:

Variant summary

Our verdict is Benign. The variant received -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_001164507.2(NEB):c.23929-45A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0113 in 1,155,992 control chromosomes in the GnomAD database, including 657 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).

Frequency

Genomes: 𝑓 0.017 ( 107 hom., cov: 32)

Exomes 𝑓: 0.011 ( 550 hom. )

Consequence

NEB
NM_001164507.2 intron

Scores

Clinical Significance

Likely benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: 0.00

Publications

2 publications found

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]

NEB links:

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]

RIF1 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.8).

BP6

Variant 2-151501528-T-C is Benign according to our data. Variant chr2-151501528-T-C is described in ClinVar as Likely_benign. ClinVar VariationId is 257800.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.136 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001164507.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
NEB	NM_001164507.2	MANE Plus Clinical	c.23929-45A>G	intron	N/A	NP_001157979.2
NEB	NM_001164508.2	MANE Select	c.23929-45A>G	intron	N/A	NP_001157980.2
NEB	NM_001271208.2		c.24034-45A>G	intron	N/A	NP_001258137.2

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
NEB	ENST00000397345.8	TSL:5 MANE Select	c.23929-45A>G	intron	N/A	ENSP00000380505.3
NEB	ENST00000427231.7	TSL:5 MANE Plus Clinical	c.23929-45A>G	intron	N/A	ENSP00000416578.2
NEB	ENST00000409198.5	TSL:5	c.18825+1265A>G	intron	N/A	ENSP00000386259.1

Frequencies

GnomAD3 genomes

AF:

0.0163

AC:

2483

AN:

152154

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0186

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00851

Gnomad ASJ

AF:

0.0314

Gnomad EAS

AF:

0.144

Gnomad SAS

AF:

0.105

Gnomad FIN

AF:

0.0000942

Gnomad MID

AF:

0.0158

Gnomad NFE

AF:

0.00231

Gnomad OTH

AF:

0.0258

GnomAD2 exomes

AF:

0.0244

AC:

1865

AN:

76294

AF XY:

0.0280

show subpopulations

Gnomad AFR exome

AF:

0.0159

Gnomad AMR exome

AF:

0.00376

Gnomad ASJ exome

AF:

0.0346

Gnomad EAS exome

AF:

0.144

Gnomad FIN exome

AF:

0.000224

Gnomad NFE exome

AF:

0.00243

Gnomad OTH exome

AF:

0.0157

GnomAD4 exome

AF:

0.0105

AC:

10558

AN:

1003720

Hom.:

550

Cov.:

AF XY:

0.0116

AC XY:

5660

AN XY:

488514

show subpopulations

African (AFR)

AF:

0.0171

AC:

373

AN:

21790

American (AMR)

AF:

0.00326

AC:

AN:

15318

Ashkenazi Jewish (ASJ)

AF:

0.0317

AC:

549

AN:

17340

East Asian (EAS)

AF:

0.137

AC:

4097

AN:

29894

South Asian (SAS)

AF:

0.0892

AC:

3078

AN:

34526

European-Finnish (FIN)

AF:

0.000661

AC:

AN:

40824

Middle Eastern (MID)

AF:

0.0150

AC:

AN:

4534

European-Non Finnish (NFE)

AF:

0.00176

AC:

1405

AN:

797950

Other (OTH)

AF:

0.0219

AC:

911

AN:

41544

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.506

Heterozygous variant carriers

456

913

1369

1826

2282

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

156

312

468

624

780

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.0165

AC:

2517

AN:

152272

Hom.:

107

Cov.:

AF XY:

0.0182

AC XY:

1358

AN XY:

74450

show subpopulations

African (AFR)

AF:

0.0188

AC:

779

AN:

41540

American (AMR)

AF:

0.00850

AC:

130

AN:

15292

Ashkenazi Jewish (ASJ)

AF:

0.0314

AC:

109

AN:

3468

East Asian (EAS)

AF:

0.145

AC:

751

AN:

5180

South Asian (SAS)

AF:

0.106

AC:

511

AN:

4828

European-Finnish (FIN)

AF:

0.0000942

AC:

AN:

10618

Middle Eastern (MID)

AF:

0.0136

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.00231

AC:

157

AN:

68024

Other (OTH)

AF:

0.0354

AC:

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

116

233

349

466

582

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

126

168

210

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.0105

Hom.:

Bravo

AF:

0.0151

Asia WGS

AF:

0.149

AC:

517

AN:

3478

ClinVar

Significance: Likely benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not specified

Benign:1

PreventionGenetics, part of Exact Sciences

Significance:Likely benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

not provided

Benign:1

Breakthrough Genomics, Breakthrough Genomics

Significance:Likely benign

Review Status:criteria provided, single submitter

Collection Method:not provided

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.80

CADD

Benign

8.4

(source)

DANN

Benign

0.69

PhyloP100

0.0

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.040

Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

Other links and lift over