Variant chr1-30873045-G-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.*166C>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 0.0869 in 643,326 control chromosomes in the GnomAD database, including 2,611 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.092 ( 678 hom., cov: 32)

Exomes 𝑓: 0.085 ( 1933 hom. )

Consequence

SDC3
NM_014654.4 3_prime_UTR

Scores

Clinical Significance

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

Conservation

PhyloP100: -2.09

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=-0.87).

BP6

Variant 1-30873045-G-A is Benign according to our data. Variant chr1-30873045-G-A is described in ClinVar as [Benign]. Clinvar id is 1289937.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.115 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.*166C>T	3_prime_UTR_variant	5/5	ENST00000339394.7	NP_055469.3	O75056
SDC3	XM_011542463.1 linkuse as main transcript	c.*166C>T	3_prime_UTR_variant	5/5		XP_011540765.1
SDC3	XM_011542464.3 linkuse as main transcript	c.*166C>T	3_prime_UTR_variant	5/5		XP_011540766.1
SDC3	XM_011542466.2 linkuse as main transcript	c.*166C>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.*166C>T		3_prime_UTR_variant	5/5	1	NM_014654.4	ENSP00000344468.6		O75056
SDC3	ENST00000336798.11 linkuse as main transcript	c.*166C>T		3_prime_UTR_variant	3/3	1		ENSP00000338346.7		A0A9K3Y886

Frequencies

GnomAD3 genomes

AF:

0.0922

AC:

14020

AN:

152132

Hom.:

677

Cov.:

show subpopulations

Gnomad AFR

AF:

0.118

Gnomad AMI

AF:

0.0396

Gnomad AMR

AF:

0.0606

Gnomad ASJ

AF:

0.0873

Gnomad EAS

AF:

0.0383

Gnomad SAS

AF:

0.0590

Gnomad FIN

AF:

0.0829

Gnomad MID

AF:

0.0981

Gnomad NFE

AF:

0.0927

Gnomad OTH

AF:

0.0891

GnomAD4 exome

AF:

0.0853

AC:

41872

AN:

491076

Hom.:

1933

Cov.:

AF XY:

0.0846

AC XY:

22103

AN XY:

261290

show subpopulations

Gnomad4 AFR exome

AF:

0.120

Gnomad4 AMR exome

AF:

0.0487

Gnomad4 ASJ exome

AF:

0.0901

Gnomad4 EAS exome

AF:

0.0357

Gnomad4 SAS exome

AF:

0.0570

Gnomad4 FIN exome

AF:

0.0946

Gnomad4 NFE exome

AF:

0.0949

Gnomad4 OTH exome

AF:

0.0904

GnomAD4 genome

AF:

0.0922

AC:

14031

AN:

152250

Hom.:

678

Cov.:

AF XY:

0.0888

AC XY:

6609

AN XY:

74458

show subpopulations

Gnomad4 AFR

AF:

0.118

Gnomad4 AMR

AF:

0.0604

Gnomad4 ASJ

AF:

0.0873

Gnomad4 EAS

AF:

0.0388

Gnomad4 SAS

AF:

0.0587

Gnomad4 FIN

AF:

0.0829

Gnomad4 NFE

AF:

0.0926

Gnomad4 OTH

AF:

0.0882

Alfa

AF:

0.0440

Hom.:

Bravo

AF:

0.0908

Asia WGS

AF:

0.0750

AC:

260

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

-0.87

CADD

Benign

0.44

DANN

Benign

0.47

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