Variant 2-20204128-A-G details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2

The NM_002997.5(SDC1):c.312T>C(p.Ala104=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00852 in 1,604,848 control chromosomes in the GnomAD database, including 73 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.0065 ( 7 hom., cov: 31)

Exomes 𝑓: 0.0087 ( 66 hom. )

Consequence

SDC1
NM_002997.5 synonymous

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -12.5

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 made for transcript

Verdict is Benign. Variant got -11 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-1.06).

BP6

Variant 2-20204128-A-G is Benign according to our data. Variant chr2-20204128-A-G is described in ClinVar as [Benign]. Clinvar id is 773122.Status of the report is criteria_provided_single_submitter, 1 stars.

BP7

Synonymous conserved (PhyloP=-12.5 with no splicing effect.

BS2

High AC in GnomAd4 at 986 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SDC1	NM_002997.5 linkuse as main transcript	c.312T>C	p.Ala104=	synonymous_variant	3/5	ENST00000254351.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SDC1	ENST00000254351.9 linkuse as main transcript	c.312T>C	p.Ala104=	synonymous_variant	3/5	1	NM_002997.5	P1

Frequencies

GnomAD3 genomes

AF:

0.00650

AC:

986

AN:

151678

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00243

Gnomad AMI

AF:

0.00439

Gnomad AMR

AF:

0.0114

Gnomad ASJ

AF:

0.00289

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00333

Gnomad FIN

AF:

0.000473

Gnomad MID

AF:

0.00637

Gnomad NFE

AF:

0.00944

Gnomad OTH

AF:

0.0163

GnomAD3 exomes

AF:

0.00652

AC:

1593

AN:

244456

Hom.:

AF XY:

0.00644

AC XY:

855

AN XY:

132782

show subpopulations

Gnomad AFR exome

AF:

0.00130

Gnomad AMR exome

AF:

0.00980

Gnomad ASJ exome

AF:

0.00289

Gnomad EAS exome

AF:

0.0000546

Gnomad SAS exome

AF:

0.00252

Gnomad FIN exome

AF:

0.000953

Gnomad NFE exome

AF:

0.00912

Gnomad OTH exome

AF:

0.0134

GnomAD4 exome

AF:

0.00873

AC:

12681

AN:

1453052

Hom.:

Cov.:

AF XY:

0.00854

AC XY:

6176

AN XY:

723188

show subpopulations

Gnomad4 AFR exome

AF:

0.00176

Gnomad4 AMR exome

AF:

0.0101

Gnomad4 ASJ exome

AF:

0.00349

Gnomad4 EAS exome

AF:

0.0000252

Gnomad4 SAS exome

AF:

0.00255

Gnomad4 FIN exome

AF:

0.00111

Gnomad4 NFE exome

AF:

0.0101

Gnomad4 OTH exome

AF:

0.00897

GnomAD4 genome

AF:

0.00650

AC:

986

AN:

151796

Hom.:

Cov.:

AF XY:

0.00619

AC XY:

459

AN XY:

74196

show subpopulations

Gnomad4 AFR

AF:

0.00242

Gnomad4 AMR

AF:

0.0114

Gnomad4 ASJ

AF:

0.00289

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00354

Gnomad4 FIN

AF:

0.000473

Gnomad4 NFE

AF:

0.00942

Gnomad4 OTH

AF:

0.0161

Alfa

AF:

0.00781

Hom.:

Bravo

AF:

0.00759

Asia WGS

AF:

0.00144

AC:

AN:

3478

EpiCase

AF:

0.0112

EpiControl

AF:

0.00996

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

Invitae

Dec 31, 2019

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-1.1

CADD

Benign

0.0070

DANN

Benign

0.49

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

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over