10-20840805-T-C

Variant names:

Variant summary

Our verdict is Benign. The variant received -17 ACMG points: 0P and 17B. BP4_StrongBP6_Very_StrongBP7BS2

The NM_006393.3(NEBL):c.1272A>G(p.Gly424Gly) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000664 in 1,610,750 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).

Frequency

Genomes: 𝑓 0.000059 ( 0 hom., cov: 32)

Exomes 𝑓: 0.000067 ( 0 hom. )

Consequence

NEBL
NM_006393.3 synonymous

Scores

Clinical Significance

Benign/Likely benign criteria provided, multiple submitters, no conflicts B:4

Conservation

PhyloP100: -0.0430

Publications

0 publications found

Variant links:

Genes affected

NEBL (HGNC:16932): (nebulette) This gene encodes a nebulin like protein that is abundantly expressed in cardiac muscle. The encoded protein binds actin and interacts with thin filaments and Z-line associated proteins in striated muscle. This protein may be involved in cardiac myofibril assembly. A shorter isoform of this protein termed LIM nebulette is expressed in non-muscle cells and may function as a component of focal adhesion complexes. Alternate splicing results in multiple transcript variants. [provided by RefSeq, Mar 2010]

NEBL Gene-Disease associations (from GenCC):

dilated cardiomyopathy
Inheritance: AD Classification: LIMITED Submitted by: ClinGen

NEBL links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -17 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.54).

BP6

Variant 10-20840805-T-C is Benign according to our data. Variant chr10-20840805-T-C is described in CliVar as Benign/Likely_benign. Clinvar id is 179438.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr10-20840805-T-C is described in CliVar as Benign/Likely_benign. Clinvar id is 179438.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr10-20840805-T-C is described in CliVar as Benign/Likely_benign. Clinvar id is 179438.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr10-20840805-T-C is described in CliVar as Benign/Likely_benign. Clinvar id is 179438.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr10-20840805-T-C is described in CliVar as Benign/Likely_benign. Clinvar id is 179438.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr10-20840805-T-C is described in CliVar as Benign/Likely_benign. Clinvar id is 179438.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr10-20840805-T-C is described in CliVar as Benign/Likely_benign. Clinvar id is 179438.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr10-20840805-T-C is described in CliVar as Benign/Likely_benign. Clinvar id is 179438.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr10-20840805-T-C is described in CliVar as Benign/Likely_benign. Clinvar id is 179438.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr10-20840805-T-C is described in CliVar as Benign/Likely_benign. Clinvar id is 179438.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr10-20840805-T-C is described in CliVar as Benign/Likely_benign. Clinvar id is 179438.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr10-20840805-T-C is described in CliVar as Benign/Likely_benign. Clinvar id is 179438.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr10-20840805-T-C is described in CliVar as Benign/Likely_benign. Clinvar id is 179438.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr10-20840805-T-C is described in CliVar as Benign/Likely_benign. Clinvar id is 179438.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr10-20840805-T-C is described in CliVar as Benign/Likely_benign. Clinvar id is 179438.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr10-20840805-T-C is described in CliVar as Benign/Likely_benign. Clinvar id is 179438.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr10-20840805-T-C is described in CliVar as Benign/Likely_benign. Clinvar id is 179438.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr10-20840805-T-C is described in CliVar as Benign/Likely_benign. Clinvar id is 179438.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr10-20840805-T-C is described in CliVar as Benign/Likely_benign. Clinvar id is 179438.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr10-20840805-T-C is described in CliVar as Benign/Likely_benign. Clinvar id is 179438.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr10-20840805-T-C is described in CliVar as Benign/Likely_benign. Clinvar id is 179438.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr10-20840805-T-C is described in CliVar as Benign/Likely_benign. Clinvar id is 179438.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr10-20840805-T-C is described in CliVar as Benign/Likely_benign. Clinvar id is 179438.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr10-20840805-T-C is described in CliVar as Benign/Likely_benign. Clinvar id is 179438.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr10-20840805-T-C is described in CliVar as Benign/Likely_benign. Clinvar id is 179438.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr10-20840805-T-C is described in CliVar as Benign/Likely_benign. Clinvar id is 179438.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=-0.043 with no splicing effect.

BS2

High AC in GnomAd4 at 9 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
NEBL	NM_006393.3 link	c.1272A>G	p.Gly424Gly	synonymous_variant	Exon 13 of 28	ENST00000377122.9	NP_006384.1	O76041-1Q59FZ8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
NEBL	ENST00000377122.9 link	c.1272A>G	p.Gly424Gly	synonymous_variant	Exon 13 of 28	1	NM_006393.3	ENSP00000366326.4		O76041-1

Frequencies

GnomAD3 genomes

AF:

0.0000592

AC:

AN:

152154

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00

Gnomad ASJ

AF:

0.00259

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00

Gnomad OTH

AF:

0.00

GnomAD2 exomes

AF:

0.000148

AC:

AN:

249834

AF XY:

0.000148

show subpopulations

Gnomad AFR exome

AF:

0.00

Gnomad AMR exome

AF:

0.0000290

Gnomad ASJ exome

AF:

0.00319

Gnomad EAS exome

AF:

0.00

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.00000886

Gnomad OTH exome

AF:

0.000492

GnomAD4 exome

AF:

0.0000672

AC:

AN:

1458596

Hom.:

Cov.:

AF XY:

0.0000620

AC XY:

AN XY:

725806

show subpopulations

African (AFR)

AF:

0.00

AC:

AN:

33398

American (AMR)

AF:

0.0000224

AC:

AN:

44622

Ashkenazi Jewish (ASJ)

AF:

0.00291

AC:

AN:

26082

East Asian (EAS)

AF:

0.00

AC:

AN:

39576

South Asian (SAS)

AF:

0.00

AC:

AN:

86160

European-Finnish (FIN)

AF:

0.00

AC:

AN:

52950

Middle Eastern (MID)

AF:

0.00

AC:

AN:

5748

European-Non Finnish (NFE)

AF:

0.0000108

AC:

AN:

1109768

Other (OTH)

AF:

0.000149

AC:

AN:

60292

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.472

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Variant carriers

<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:

0.0000592

AC:

AN:

152154

Hom.:

Cov.:

AF XY:

0.0000672

AC XY:

AN XY:

74352

show subpopulations

African (AFR)

AF:

0.00

AC:

AN:

41416

American (AMR)

AF:

0.00

AC:

AN:

15262

Ashkenazi Jewish (ASJ)

AF:

0.00259

AC:

AN:

3472

East Asian (EAS)

AF:

0.00

AC:

AN:

5204

South Asian (SAS)

AF:

0.00

AC:

AN:

4836

European-Finnish (FIN)

AF:

0.00

AC:

AN:

10622

Middle Eastern (MID)

AF:

0.00

AC:

AN:

316

European-Non Finnish (NFE)

AF:

0.00

AC:

AN:

68020

Other (OTH)

AF:

0.00

AC:

AN:

2094

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.458

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Variant carriers

<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:

0.000405

Hom.:

Bravo

AF:

0.0000604

ClinVar

Significance: Benign/Likely benign

Submissions summary: Benign:4

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not specified

Benign:2

Feb 11, 2022

Ambry Genetics

Significance:Likely benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. -

Dec 20, 2013

Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine

Significance:Likely benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

Gly424Gly in exon 13 of NEBL: This variant is not expected to have clinical sign ificance because it does not alter an amino acid residue and is not located with in the splice consensus sequence. Gly424Gly in exon 13 of NEBL (allele frequenc y = n/a) -

not provided

Benign:1

May 19, 2020

GeneDx

Significance:Likely benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

Primary dilated cardiomyopathy

Benign:1

Oct 24, 2024

Labcorp Genetics (formerly Invitae), Labcorp

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.54

CADD

Benign

8.4

(source)

DANN

Benign

0.72

PhyloP100

-0.043

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

Other links and lift over