Variant chr2-20204188-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1

The NM_002997.5(SDC1):c.252G>A(p.Glu84=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.247 in 1,599,504 control chromosomes in the GnomAD database, including 50,140 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 0.22 ( 4045 hom., cov: 30)

Exomes 𝑓: 0.25 ( 46095 hom. )

Consequence

SDC1
NM_002997.5 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -4.65

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 -13 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.81).

BP7

Synonymous conserved (PhyloP=-4.65 with no splicing effect.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.259 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SDC1	NM_002997.5 linkuse as main transcript	c.252G>A	p.Glu84=	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.252G>A	p.Glu84=	synonymous_variant	3/5	1	NM_002997.5	P1

Frequencies

GnomAD3 genomes

AF:

0.225

AC:

34122

AN:

151830

Hom.:

4043

Cov.:

show subpopulations

Gnomad AFR

AF:

0.170

Gnomad AMI

AF:

0.113

Gnomad AMR

AF:

0.211

Gnomad ASJ

AF:

0.316

Gnomad EAS

AF:

0.100

Gnomad SAS

AF:

0.169

Gnomad FIN

AF:

0.280

Gnomad MID

AF:

0.247

Gnomad NFE

AF:

0.262

Gnomad OTH

AF:

0.235

GnomAD3 exomes

AF:

0.225

AC:

54061

AN:

240036

Hom.:

6492

AF XY:

0.227

AC XY:

29640

AN XY:

130584

show subpopulations

Gnomad AFR exome

AF:

0.169

Gnomad AMR exome

AF:

0.209

Gnomad ASJ exome

AF:

0.314

Gnomad EAS exome

AF:

0.103

Gnomad SAS exome

AF:

0.180

Gnomad FIN exome

AF:

0.276

Gnomad NFE exome

AF:

0.255

Gnomad OTH exome

AF:

0.252

GnomAD4 exome

AF:

0.249

AC:

360569

AN:

1447556

Hom.:

46095

Cov.:

AF XY:

0.248

AC XY:

178363

AN XY:

720566

show subpopulations

Gnomad4 AFR exome

AF:

0.170

Gnomad4 AMR exome

AF:

0.211

Gnomad4 ASJ exome

AF:

0.318

Gnomad4 EAS exome

AF:

0.104

Gnomad4 SAS exome

AF:

0.176

Gnomad4 FIN exome

AF:

0.263

Gnomad4 NFE exome

AF:

0.262

Gnomad4 OTH exome

AF:

0.246

GnomAD4 genome

AF:

0.225

AC:

34126

AN:

151948

Hom.:

4045

Cov.:

AF XY:

0.225

AC XY:

16690

AN XY:

74254

show subpopulations

Gnomad4 AFR

AF:

0.170

Gnomad4 AMR

AF:

0.211

Gnomad4 ASJ

AF:

0.316

Gnomad4 EAS

AF:

0.100

Gnomad4 SAS

AF:

0.169

Gnomad4 FIN

AF:

0.280

Gnomad4 NFE

AF:

0.262

Gnomad4 OTH

AF:

0.233

Alfa

AF:

0.201

Hom.:

744

Bravo

AF:

0.220

Asia WGS

AF:

0.137

AC:

476

AN:

3478

EpiCase

AF:

0.258

EpiControl

AF:

0.259

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.81

CADD

Benign

0.045

DANN

Benign

0.55

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.030

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

Computational scores

Splicing

Publications

LitVar

Other links and lift over