dbSNP rs1131351: SDC1:c.*147G>C (chr2-20202619-C-G) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_002997.5(SDC1):c.*147G>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.434 in 773,762 control chromosomes in the GnomAD database, including 74,640 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 0.40 ( 12632 hom., cov: 31)

Exomes 𝑓: 0.44 ( 62008 hom. )

Consequence

SDC1
NM_002997.5 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0400

Publications

16 publications found

Variant links:

Genes affected

SDC1 (HGNC:10658): (syndecan 1) The protein encoded by this gene is a transmembrane (type I) heparan sulfate proteoglycan and is a member of the syndecan proteoglycan family. The syndecans mediate cell binding, cell signaling, and cytoskeletal organization and syndecan receptors are required for internalization of the HIV-1 tat protein. The syndecan-1 protein functions as an integral membrane protein and participates in cell proliferation, cell migration and cell-matrix interactions via its receptor for extracellular matrix proteins. Altered syndecan-1 expression has been detected in several different tumor types. While several transcript variants may exist for this gene, the full-length natures of only two have been described to date. These two represent the major variants of this gene and encode the same protein. [provided by RefSeq, Jul 2008]

SDC1 links:

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.67).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.442 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SDC1	NM_002997.5 link	c.*147G>C		3_prime_UTR_variant	Exon 5 of 5	ENST00000254351.9	NP_002988.4	P18827

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein	UniProt
SDC1	ENST00000254351.9 link	c.*147G>C	3_prime_UTR_variant	Exon 5 of 5	1	NM_002997.5	ENSP00000254351.4	P18827
SDC1	ENST00000403076.5 link	c.479-318G>C	intron_variant	Intron 3 of 3	1		ENSP00000384613.1	E9PHH3
SDC1	ENST00000381150.5 link	c.*147G>C	3_prime_UTR_variant	Exon 6 of 6	5		ENSP00000370542.1	P18827

Frequencies

GnomAD3 genomes

AF:

0.397

AC:

60268

AN:

151902

Hom.:

12616

Cov.:

show subpopulations

Gnomad AFR

AF:

0.265

Gnomad AMI

AF:

0.387

Gnomad AMR

AF:

0.400

Gnomad ASJ

AF:

0.365

Gnomad EAS

AF:

0.410

Gnomad SAS

AF:

0.451

Gnomad FIN

AF:

0.575

Gnomad MID

AF:

0.259

Gnomad NFE

AF:

0.446

Gnomad OTH

AF:

0.383

GnomAD4 exome

AF:

0.443

AC:

275546

AN:

621740

Hom.:

62008

Cov.:

AF XY:

0.442

AC XY:

143845

AN XY:

325178

show subpopulations

African (AFR)

AF:

0.268

AC:

4312

AN:

16110

American (AMR)

AF:

0.433

AC:

11454

AN:

26472

Ashkenazi Jewish (ASJ)

AF:

0.368

AC:

5572

AN:

15138

East Asian (EAS)

AF:

0.378

AC:

13221

AN:

34976

South Asian (SAS)

AF:

0.433

AC:

22435

AN:

51850

European-Finnish (FIN)

AF:

0.554

AC:

21806

AN:

39362

Middle Eastern (MID)

AF:

0.310

AC:

745

AN:

2404

European-Non Finnish (NFE)

AF:

0.452

AC:

182313

AN:

403584

Other (OTH)

AF:

0.430

AC:

13688

AN:

31844

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.512

Heterozygous variant carriers

7926

15852

23777

31703

39629

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.397

AC:

60314

AN:

152022

Hom.:

12632

Cov.:

AF XY:

0.404

AC XY:

30040

AN XY:

74298

show subpopulations

African (AFR)

AF:

0.265

AC:

10992

AN:

41468

American (AMR)

AF:

0.401

AC:

6123

AN:

15278

Ashkenazi Jewish (ASJ)

AF:

0.365

AC:

1265

AN:

3470

East Asian (EAS)

AF:

0.411

AC:

2111

AN:

5142

South Asian (SAS)

AF:

0.452

AC:

2174

AN:

4812

European-Finnish (FIN)

AF:

0.575

AC:

6075

AN:

10566

Middle Eastern (MID)

AF:

0.265

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.446

AC:

30342

AN:

67968

Other (OTH)

AF:

0.379

AC:

801

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.508

Heterozygous variant carriers

1817

3634

5450

7267

9084

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Alfa

AF:

0.302

Hom.:

898

Bravo

AF:

0.380

Asia WGS

AF:

0.404

AC:

1403

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.67

CADD

Benign

7.3

(source)

DANN

Benign

0.88

PhyloP100

-0.040

Mutation Taster

=100/0

polymorphism (auto)

(source)

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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rs1131351

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