Variant 1-30874592-C-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2

The NM_014654.4(SDC3):c.871-4G>T variant causes a splice region, splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00285 in 1,612,998 control chromosomes in the GnomAD database, including 81 homozygotes. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.0047 ( 22 hom., cov: 32)

Exomes 𝑓: 0.0026 ( 59 hom. )

Consequence

SDC3
NM_014654.4 splice_region, splice_polypyrimidine_tract, intron

Scores

Splicing: ADA: 0.0003116

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -1.07

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:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.63).

BP6

Variant 1-30874592-C-A is Benign according to our data. Variant chr1-30874592-C-A is described in ClinVar as [Benign]. Clinvar id is 737823.Status of the report is criteria_provided_single_submitter, 1 stars.

BS2

High AC in GnomAd4 at 719 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	MANE
SDC3	NM_014654.4 linkuse as main transcript	c.871-4G>T	splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant	ENST00000339394.7
SDC3	XM_011542463.1 linkuse as main transcript	c.838-4G>T	splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant
SDC3	XM_011542464.3 linkuse as main transcript	c.835-4G>T	splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant
SDC3	XM_011542466.2 linkuse as main transcript	c.745-4G>T	splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SDC3	ENST00000339394.7 linkuse as main transcript	c.871-4G>T		splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant		1	NM_014654.4	P1
SDC3	ENST00000336798.11 linkuse as main transcript	c.697-4G>T		splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant		1

Frequencies

GnomAD3 genomes

AF:

0.00472

AC:

719

AN:

152180

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00

Gnomad AMI

AF:

0.00110

Gnomad AMR

AF:

0.00

Gnomad ASJ

AF:

0.00893

Gnomad EAS

AF:

0.000963

Gnomad SAS

AF:

0.000207

Gnomad FIN

AF:

0.0554

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00135

Gnomad OTH

AF:

0.000478

GnomAD3 exomes

AF:

0.00651

AC:

1624

AN:

249574

Hom.:

AF XY:

0.00644

AC XY:

868

AN XY:

134848

show subpopulations

Gnomad AFR exome

AF:

0.000123

Gnomad AMR exome

AF:

0.0000290

Gnomad ASJ exome

AF:

0.00857

Gnomad EAS exome

AF:

0.00131

Gnomad SAS exome

AF:

0.000920

Gnomad FIN exome

AF:

0.0560

Gnomad NFE exome

AF:

0.00216

Gnomad OTH exome

AF:

0.00590

GnomAD4 exome

AF:

0.00265

AC:

3870

AN:

1460700

Hom.:

Cov.:

AF XY:

0.00265

AC XY:

1928

AN XY:

726570

show subpopulations

Gnomad4 AFR exome

AF:

0.0000598

Gnomad4 AMR exome

AF:

0.0000448

Gnomad4 ASJ exome

AF:

0.00938

Gnomad4 EAS exome

AF:

0.00217

Gnomad4 SAS exome

AF:

0.000673

Gnomad4 FIN exome

AF:

0.0501

Gnomad4 NFE exome

AF:

0.000544

Gnomad4 OTH exome

AF:

0.00323

GnomAD4 genome

AF:

0.00472

AC:

719

AN:

152298

Hom.:

Cov.:

AF XY:

0.00685

AC XY:

510

AN XY:

74454

show subpopulations

Gnomad4 AFR

AF:

0.00

Gnomad4 AMR

AF:

0.00

Gnomad4 ASJ

AF:

0.00893

Gnomad4 EAS

AF:

0.000965

Gnomad4 SAS

AF:

0.000207

Gnomad4 FIN

AF:

0.0554

Gnomad4 NFE

AF:

0.00135

Gnomad4 OTH

AF:

0.000473

Alfa

AF:

0.00224

Hom.:

Bravo

AF:

0.000744

Asia WGS

AF:

0.00318

AC:

AN:

3478

EpiCase

AF:

0.000491

EpiControl

AF:

0.000593

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

Jun 14, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.63

CADD

Benign

7.5

DANN

Benign

0.82

Splicing

Name

Calibrated prediction

Score

Prediction

dbscSNV1_ADA

Benign

0.00031

dbscSNV1_RF

Benign

0.036

SpliceAI score (max)

0.020

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