NM_015374.3:c.396G>A

Variant names:

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 0P and 2B. BP6_Moderate

The NM_015374.3(SUN2):c.396G>A(p.Ser132Ser) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000242 in 1,614,034 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 0.00012 ( 0 hom., cov: 33)

Exomes 𝑓: 0.000014 ( 0 hom. )

Consequence

SUN2
NM_015374.3 synonymous

Scores

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: -4.61

Publications

0 publications found

Variant links:

Genes affected

SUN2 (HGNC:14210): (Sad1 and UNC84 domain containing 2) SUN1 (MIM 607723) and SUN2 are inner nuclear membrane (INM) proteins that play a major role in nuclear-cytoplasmic connection by formation of a 'bridge' across the nuclear envelope, known as the LINC complex, via interaction with the conserved luminal KASH domain of nesprins (e.g., SYNE1; MIM 608441) located in the outer nuclear membrane (ONM). The LINC complex provides a direct connection between the nuclear lamina and the cytoskeleton, which contributes to nuclear positioning and cellular rigidity (summary by Haque et al., 2010 [PubMed 19933576]).[supplied by OMIM, Nov 2010]

SUN2 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Likely_benign. The variant received -2 ACMG points.

BP6

Variant 22-38750926-C-T is Benign according to our data. Variant chr22-38750926-C-T is described in CliVar as Likely_benign. Clinvar id is 461686.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr22-38750926-C-T is described in CliVar as Likely_benign. Clinvar id is 461686.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr22-38750926-C-T is described in CliVar as Likely_benign. Clinvar id is 461686.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr22-38750926-C-T is described in CliVar as Likely_benign. Clinvar id is 461686.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr22-38750926-C-T is described in CliVar as Likely_benign. Clinvar id is 461686.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr22-38750926-C-T is described in CliVar as Likely_benign. Clinvar id is 461686.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr22-38750926-C-T is described in CliVar as Likely_benign. Clinvar id is 461686.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr22-38750926-C-T is described in CliVar as Likely_benign. Clinvar id is 461686.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr22-38750926-C-T is described in CliVar as Likely_benign. Clinvar id is 461686.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr22-38750926-C-T is described in CliVar as Likely_benign. Clinvar id is 461686.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr22-38750926-C-T is described in CliVar as Likely_benign. Clinvar id is 461686.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr22-38750926-C-T is described in CliVar as Likely_benign. Clinvar id is 461686.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr22-38750926-C-T is described in CliVar as Likely_benign. Clinvar id is 461686.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr22-38750926-C-T is described in CliVar as Likely_benign. Clinvar id is 461686.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr22-38750926-C-T is described in CliVar as Likely_benign. Clinvar id is 461686.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr22-38750926-C-T is described in CliVar as Likely_benign. Clinvar id is 461686.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr22-38750926-C-T is described in CliVar as Likely_benign. Clinvar id is 461686.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr22-38750926-C-T is described in CliVar as Likely_benign. Clinvar id is 461686.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr22-38750926-C-T is described in CliVar as Likely_benign. Clinvar id is 461686.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr22-38750926-C-T is described in CliVar as Likely_benign. Clinvar id is 461686.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr22-38750926-C-T is described in CliVar as Likely_benign. Clinvar id is 461686.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr22-38750926-C-T is described in CliVar as Likely_benign. Clinvar id is 461686.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr22-38750926-C-T is described in CliVar as Likely_benign. Clinvar id is 461686.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr22-38750926-C-T is described in CliVar as Likely_benign. Clinvar id is 461686.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr22-38750926-C-T is described in CliVar as Likely_benign. Clinvar id is 461686.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr22-38750926-C-T is described in CliVar as Likely_benign. Clinvar id is 461686.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr22-38750926-C-T is described in CliVar as Likely_benign. Clinvar id is 461686.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr22-38750926-C-T is described in CliVar as Likely_benign. Clinvar id is 461686.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr22-38750926-C-T is described in CliVar as Likely_benign. Clinvar id is 461686.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr22-38750926-C-T is described in CliVar as Likely_benign. Clinvar id is 461686.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr22-38750926-C-T is described in CliVar as Likely_benign. Clinvar id is 461686.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr22-38750926-C-T is described in CliVar as Likely_benign. Clinvar id is 461686.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr22-38750926-C-T is described in CliVar as Likely_benign. Clinvar id is 461686.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr22-38750926-C-T is described in CliVar as Likely_benign. Clinvar id is 461686.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr22-38750926-C-T is described in CliVar as Likely_benign. Clinvar id is 461686.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr22-38750926-C-T is described in CliVar as Likely_benign. Clinvar id is 461686.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr22-38750926-C-T is described in CliVar as Likely_benign. Clinvar id is 461686.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr22-38750926-C-T is described in CliVar as Likely_benign. Clinvar id is 461686.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr22-38750926-C-T is described in CliVar as Likely_benign. Clinvar id is 461686.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr22-38750926-C-T is described in CliVar as Likely_benign. Clinvar id is 461686.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr22-38750926-C-T is described in CliVar as Likely_benign. Clinvar id is 461686.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr22-38750926-C-T is described in CliVar as Likely_benign. Clinvar id is 461686.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr22-38750926-C-T is described in CliVar as Likely_benign. Clinvar id is 461686.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr22-38750926-C-T is described in CliVar as Likely_benign. Clinvar id is 461686.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr22-38750926-C-T is described in CliVar as Likely_benign. Clinvar id is 461686.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr22-38750926-C-T is described in CliVar as Likely_benign. Clinvar id is 461686.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr22-38750926-C-T is described in CliVar as Likely_benign. Clinvar id is 461686.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr22-38750926-C-T is described in CliVar as Likely_benign. Clinvar id is 461686.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr22-38750926-C-T is described in CliVar as Likely_benign. Clinvar id is 461686.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr22-38750926-C-T is described in CliVar as Likely_benign. Clinvar id is 461686.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr22-38750926-C-T is described in CliVar as Likely_benign. Clinvar id is 461686.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr22-38750926-C-T is described in CliVar as Likely_benign. Clinvar id is 461686.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr22-38750926-C-T is described in CliVar as Likely_benign. Clinvar id is 461686.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr22-38750926-C-T is described in CliVar as Likely_benign. Clinvar id is 461686.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr22-38750926-C-T is described in CliVar as Likely_benign. Clinvar id is 461686.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr22-38750926-C-T is described in CliVar as Likely_benign. Clinvar id is 461686.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr22-38750926-C-T is described in CliVar as Likely_benign. Clinvar id is 461686.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr22-38750926-C-T is described in CliVar as Likely_benign. Clinvar id is 461686.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr22-38750926-C-T is described in CliVar as Likely_benign. Clinvar id is 461686.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr22-38750926-C-T is described in CliVar as Likely_benign. Clinvar id is 461686.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr22-38750926-C-T is described in CliVar as Likely_benign. Clinvar id is 461686.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr22-38750926-C-T is described in CliVar as Likely_benign. Clinvar id is 461686.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr22-38750926-C-T is described in CliVar as Likely_benign. Clinvar id is 461686.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr22-38750926-C-T is described in CliVar as Likely_benign. Clinvar id is 461686.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr22-38750926-C-T is described in CliVar as Likely_benign. Clinvar id is 461686.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr22-38750926-C-T is described in CliVar as Likely_benign. Clinvar id is 461686.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr22-38750926-C-T is described in CliVar as Likely_benign. Clinvar id is 461686.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr22-38750926-C-T is described in CliVar as Likely_benign. Clinvar id is 461686.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr22-38750926-C-T is described in CliVar as Likely_benign. Clinvar id is 461686.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr22-38750926-C-T is described in CliVar as Likely_benign. Clinvar id is 461686.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr22-38750926-C-T is described in CliVar as Likely_benign. Clinvar id is 461686.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr22-38750926-C-T is described in CliVar as Likely_benign. Clinvar id is 461686.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr22-38750926-C-T is described in CliVar as Likely_benign. Clinvar id is 461686.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr22-38750926-C-T is described in CliVar as Likely_benign. Clinvar id is 461686.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr22-38750926-C-T is described in CliVar as Likely_benign. Clinvar id is 461686.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr22-38750926-C-T is described in CliVar as Likely_benign. Clinvar id is 461686.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr22-38750926-C-T is described in CliVar as Likely_benign. Clinvar id is 461686.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr22-38750926-C-T is described in CliVar as Likely_benign. Clinvar id is 461686.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr22-38750926-C-T is described in CliVar as Likely_benign. Clinvar id is 461686.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr22-38750926-C-T is described in CliVar as Likely_benign. Clinvar id is 461686.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr22-38750926-C-T is described in CliVar as Likely_benign. Clinvar id is 461686.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr22-38750926-C-T is described in CliVar as Likely_benign. Clinvar id is 461686.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr22-38750926-C-T is described in CliVar as Likely_benign. Clinvar id is 461686.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr22-38750926-C-T is described in CliVar as Likely_benign. Clinvar id is 461686.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr22-38750926-C-T is described in CliVar as Likely_benign. Clinvar id is 461686.Status of the report is criteria_provided_single_submitter, 1 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SUN2	NM_015374.3 link	c.396G>A	p.Ser132Ser	synonymous_variant	Exon 4 of 18	ENST00000689035.1	NP_056189.1	Q9UH99-1A0A024R1P7B4E2A6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SUN2	ENST00000689035.1 link	c.396G>A	p.Ser132Ser	synonymous_variant	Exon 4 of 18		NM_015374.3	ENSP00000508608.1		Q9UH99-1

Frequencies

GnomAD3 genomes

AF:

0.000125

AC:

AN:

152206

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000386

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.000414

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.0000147

Gnomad OTH

AF:

0.00

GnomAD2 exomes

AF:

0.0000558

AC:

AN:

250868

AF XY:

0.0000442

show subpopulations

Gnomad AFR exome

AF:

0.000494

Gnomad AMR exome

AF:

0.0000579

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.00

Gnomad FIN exome

AF:

0.0000463

Gnomad NFE exome

AF:

0.00

Gnomad OTH exome

AF:

0.00

GnomAD4 exome

AF:

0.0000137

AC:

AN:

1461710

Hom.:

Cov.:

AF XY:

0.0000151

AC XY:

AN XY:

727168

show subpopulations

African (AFR)

AF:

0.000239

AC:

AN:

33478

American (AMR)

AF:

0.0000671

AC:

AN:

44718

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

26136

East Asian (EAS)

AF:

0.00

AC:

AN:

39696

South Asian (SAS)

AF:

0.0000464

AC:

AN:

86256

European-Finnish (FIN)

AF:

0.0000376

AC:

AN:

53260

Middle Eastern (MID)

AF:

0.000173

AC:

AN:

5766

European-Non Finnish (NFE)

AF:

8.99e-7

AC:

AN:

1112004

Other (OTH)

AF:

0.0000166

AC:

AN:

60396

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.465

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:

0.000125

AC:

AN:

152324

Hom.:

Cov.:

AF XY:

0.000107

AC XY:

AN XY:

74492

show subpopulations

African (AFR)

AF:

0.000385

AC:

AN:

41570

American (AMR)

AF:

0.00

AC:

AN:

15310

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

3472

East Asian (EAS)

AF:

0.00

AC:

AN:

5186

South Asian (SAS)

AF:

0.000415

AC:

AN:

4822

European-Finnish (FIN)

AF:

0.00

AC:

AN:

10626

Middle Eastern (MID)

AF:

0.00

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0000147

AC:

AN:

68016

Other (OTH)

AF:

0.00

AC:

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.541

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:

0.0000658

Hom.:

Bravo

AF:

0.000151

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

Emery-Dreifuss muscular dystrophy

Benign:1

Dec 22, 2023

Labcorp Genetics (formerly Invitae), Labcorp

Significance:Likely 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

-0.59

CADD

Benign

4.0

(source)

DANN

Benign

0.92

PhyloP100

-4.6

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.7

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.29

Details are displayed if max score is > 0.2

DS_AG_spliceai

0.29

Position offset: -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

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