Variant 1-30872938-T-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_014654.4(SDC3):c.*273A>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0745 in 441,146 control chromosomes in the GnomAD database, including 1,445 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.065 ( 396 hom., cov: 32)

Exomes 𝑓: 0.079 ( 1049 hom. )

Consequence

SDC3
NM_014654.4 3_prime_UTR

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: -0.358

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 made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.79).

BP6

Variant 1-30872938-T-A is Benign according to our data. Variant chr1-30872938-T-A is described in ClinVar as [Benign]. Clinvar id is 1287484.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0903 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	#exon/exons	MANE	Protein	UniProt
SDC3	NM_014654.4 linkuse as main transcript	c.*273A>T	3_prime_UTR_variant	5/5	ENST00000339394.7	NP_055469.3	O75056
SDC3	XM_011542463.1 linkuse as main transcript	c.*273A>T	3_prime_UTR_variant	5/5		XP_011540765.1
SDC3	XM_011542464.3 linkuse as main transcript	c.*273A>T	3_prime_UTR_variant	5/5		XP_011540766.1
SDC3	XM_011542466.2 linkuse as main transcript	c.*273A>T	3_prime_UTR_variant	5/5		XP_011540768.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SDC3	ENST00000339394 linkuse as main transcript	c.*273A>T		3_prime_UTR_variant	5/5	1	NM_014654.4	ENSP00000344468.6		O75056
SDC3	ENST00000336798.11 linkuse as main transcript	c.*273A>T		3_prime_UTR_variant	3/3	1		ENSP00000338346.7		A0A9K3Y886

Frequencies

GnomAD3 genomes

AF:

0.0652

AC:

9913

AN:

152074

Hom.:

396

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0256

Gnomad AMI

AF:

0.0395

Gnomad AMR

AF:

0.0502

Gnomad ASJ

AF:

0.0691

Gnomad EAS

AF:

0.0382

Gnomad SAS

AF:

0.0589

Gnomad FIN

AF:

0.0825

Gnomad MID

AF:

0.101

Gnomad NFE

AF:

0.0922

Gnomad OTH

AF:

0.0712

GnomAD4 exome

AF:

0.0794

AC:

22941

AN:

288954

Hom.:

1049

Cov.:

AF XY:

0.0793

AC XY:

11761

AN XY:

148384

show subpopulations

Gnomad4 AFR exome

AF:

0.0229

Gnomad4 AMR exome

AF:

0.0464

Gnomad4 ASJ exome

AF:

0.0724

Gnomad4 EAS exome

AF:

0.0348

Gnomad4 SAS exome

AF:

0.0523

Gnomad4 FIN exome

AF:

0.0926

Gnomad4 NFE exome

AF:

0.0913

Gnomad4 OTH exome

AF:

0.0779

GnomAD4 genome

AF:

0.0651

AC:

9913

AN:

152192

Hom.:

396

Cov.:

AF XY:

0.0633

AC XY:

4708

AN XY:

74406

show subpopulations

Gnomad4 AFR

AF:

0.0256

Gnomad4 AMR

AF:

0.0502

Gnomad4 ASJ

AF:

0.0691

Gnomad4 EAS

AF:

0.0387

Gnomad4 SAS

AF:

0.0587

Gnomad4 FIN

AF:

0.0825

Gnomad4 NFE

AF:

0.0922

Gnomad4 OTH

AF:

0.0704

Alfa

AF:

0.0888

Hom.:

Bravo

AF:

0.0596

Asia WGS

AF:

0.0700

AC:

245

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	Jun 19, 2021	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.79

CADD

Benign

3.1

DANN

Benign

0.73

Splicing

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