dbSNP rs1539360: SDC3:p.Gly396Gly (chr1-30873352-G-A) – ACMG Classification: Benign (-11 pts)

Variant summary

Our verdict is Benign. The variant received -11 ACMG points: 0P and 11B. BP4_ModerateBP7BA1

The NM_014654.4(SDC3):c.1188C>T(p.Gly396Gly) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.103 in 1,612,534 control chromosomes in the GnomAD database, including 9,309 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.080 ( 653 hom., cov: 32)

Exomes 𝑓: 0.10 ( 8656 hom. )

Consequence

SDC3
NM_014654.4 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.340

Publications

9 publications found

Variant links:

Genes affected

SDC3 (HGNC:10660): (syndecan 3) The protein encoded by this gene belongs to the syndecan proteoglycan family. It may play a role in the organization of cell shape by affecting the actin cytoskeleton, possibly by transferring signals from the cell surface in a sugar-dependent mechanism. Allelic variants of this gene have been associated with obesity. [provided by RefSeq, Oct 2009]

SDC3 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -11 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.34).

BP7

Synonymous conserved (PhyloP=-0.34 with no splicing effect.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.115 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein
SDC3	NM_014654.4 link	c.1188C>T	p.Gly396Gly	synonymous_variant	Exon 5 of 5	ENST00000339394.7	NP_055469.3
SDC3	XM_011542463.1 link	c.1155C>T	p.Gly385Gly	synonymous_variant	Exon 5 of 5		XP_011540765.1
SDC3	XM_011542464.3 link	c.1152C>T	p.Gly384Gly	synonymous_variant	Exon 5 of 5		XP_011540766.1
SDC3	XM_011542466.2 link	c.1062C>T	p.Gly354Gly	synonymous_variant	Exon 5 of 5		XP_011540768.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SDC3	ENST00000339394.7 link	c.1188C>T	p.Gly396Gly	synonymous_variant	Exon 5 of 5	1	NM_014654.4	ENSP00000344468.6
SDC3	ENST00000336798.11 link	c.1014C>T	p.Gly338Gly	synonymous_variant	Exon 3 of 3	1		ENSP00000338346.7

Frequencies

GnomAD3 genomes

AF:

0.0805

AC:

12232

AN:

152010

Hom.:

653

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0206

Gnomad AMI

AF:

0.111

Gnomad AMR

AF:

0.0624

Gnomad ASJ

AF:

0.0806

Gnomad EAS

AF:

0.0795

Gnomad SAS

AF:

0.0567

Gnomad FIN

AF:

0.115

Gnomad MID

AF:

0.0823

Gnomad NFE

AF:

0.117

Gnomad OTH

AF:

0.0767

GnomAD2 exomes

AF:

0.0892

AC:

22399

AN:

251216

AF XY:

0.0910

show subpopulations

Gnomad AFR exome

AF:

0.0175

Gnomad AMR exome

AF:

0.0434

Gnomad ASJ exome

AF:

0.0881

Gnomad EAS exome

AF:

0.0799

Gnomad FIN exome

AF:

0.123

Gnomad NFE exome

AF:

0.116

Gnomad OTH exome

AF:

0.0968

GnomAD4 exome

AF:

0.105

AC:

153303

AN:

1460406

Hom.:

8656

Cov.:

AF XY:

0.104

AC XY:

75309

AN XY:

726590

show subpopulations

African (AFR)

AF:

0.0148

AC:

495

AN:

33466

American (AMR)

AF:

0.0452

AC:

2023

AN:

44720

Ashkenazi Jewish (ASJ)

AF:

0.0860

AC:

2246

AN:

26122

East Asian (EAS)

AF:

0.0594

AC:

2358

AN:

39690

South Asian (SAS)

AF:

0.0626

AC:

5401

AN:

86234

European-Finnish (FIN)

AF:

0.124

AC:

6624

AN:

53406

Middle Eastern (MID)

AF:

0.0825

AC:

475

AN:

5760

European-Non Finnish (NFE)

AF:

0.115

AC:

127785

AN:

1110666

Other (OTH)

AF:

0.0977

AC:

5896

AN:

60342

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.470

Heterozygous variant carriers

6290

12580

18870

25160

31450

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

4506

9012

13518

18024

22530

<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:

0.0804

AC:

12231

AN:

152128

Hom.:

653

Cov.:

AF XY:

0.0792

AC XY:

5891

AN XY:

74358

show subpopulations

African (AFR)

AF:

0.0206

AC:

853

AN:

41506

American (AMR)

AF:

0.0622

AC:

952

AN:

15296

Ashkenazi Jewish (ASJ)

AF:

0.0806

AC:

280

AN:

3472

East Asian (EAS)

AF:

0.0795

AC:

410

AN:

5160

South Asian (SAS)

AF:

0.0574

AC:

276

AN:

4808

European-Finnish (FIN)

AF:

0.115

AC:

1214

AN:

10582

Middle Eastern (MID)

AF:

0.0782

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.117

AC:

7960

AN:

67990

Other (OTH)

AF:

0.0769

AC:

162

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

567

1134

1702

2269

2836

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

148

296

444

592

740

<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:

0.0881

Hom.:

692

Bravo

AF:

0.0741

Asia WGS

AF:

0.0810

AC:

280

AN:

3478

EpiCase

AF:

0.116

EpiControl

AF:

0.114

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.34

CADD

Benign

9.9

(source)

DANN

Benign

0.70

PhyloP100

-0.34

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.7

Mutation Taster

=96/4

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.050

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

Computational scores

Splicing

Publications

Other links and lift over