Variant 5-151676076-C-G details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1

The NM_003118.4(SPARC):c.57+56G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0932 in 1,450,910 control chromosomes in the GnomAD database, including 10,201 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.16 ( 3511 hom., cov: 32)

Exomes 𝑓: 0.085 ( 6690 hom. )

Consequence

SPARC
NM_003118.4 intron

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.0470

Variant links:

Genes affected

SPARC (HGNC:11219): (secreted protein acidic and cysteine rich) This gene encodes a cysteine-rich acidic matrix-associated protein. The encoded protein is required for the collagen in bone to become calcified but is also involved in extracellular matrix synthesis and promotion of changes to cell shape. The gene product has been associated with tumor suppression but has also been correlated with metastasis based on changes to cell shape which can promote tumor cell invasion. Three transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jun 2015]

SPARC links:

SPARC (HGNC:):

SPARC links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.85).

BP6

Variant 5-151676076-C-G is Benign according to our data. Variant chr5-151676076-C-G is described in ClinVar as [Benign]. Clinvar id is 1281906.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.381 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	MANE	Protein	UniProt
SPARC	NM_003118.4 linkuse as main transcript	c.57+56G>C	intron_variant	ENST00000231061.9	NP_003109.1	P09486
SPARC	NM_001309444.2 linkuse as main transcript	c.57+56G>C	intron_variant		NP_001296373.1	P09486
SPARC	NM_001309443.2 linkuse as main transcript	c.57+56G>C	intron_variant		NP_001296372.1	P09486

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SPARC	ENST00000231061.9 linkuse as main transcript	c.57+56G>C		intron_variant		1	NM_003118.4	ENSP00000231061.4		P09486

Frequencies

GnomAD3 genomes

AF:

0.163

AC:

24755

AN:

151904

Hom.:

3494

Cov.:

show subpopulations

Gnomad AFR

AF:

0.386

Gnomad AMI

AF:

0.0307

Gnomad AMR

AF:

0.0896

Gnomad ASJ

AF:

0.0898

Gnomad EAS

AF:

0.0650

Gnomad SAS

AF:

0.139

Gnomad FIN

AF:

0.0886

Gnomad MID

AF:

0.0981

Gnomad NFE

AF:

0.0713

Gnomad OTH

AF:

0.144

GnomAD4 exome

AF:

0.0850

AC:

110359

AN:

1298890

Hom.:

6690

AF XY:

0.0860

AC XY:

55924

AN XY:

650082

show subpopulations

Gnomad4 AFR exome

AF:

0.401

Gnomad4 AMR exome

AF:

0.0577

Gnomad4 ASJ exome

AF:

0.0781

Gnomad4 EAS exome

AF:

0.0750

Gnomad4 SAS exome

AF:

0.137

Gnomad4 FIN exome

AF:

0.0795

Gnomad4 NFE exome

AF:

0.0721

Gnomad4 OTH exome

AF:

0.0966

GnomAD4 genome

AF:

0.163

AC:

24810

AN:

152020

Hom.:

3511

Cov.:

AF XY:

0.162

AC XY:

12027

AN XY:

74296

show subpopulations

Gnomad4 AFR

AF:

0.386

Gnomad4 AMR

AF:

0.0894

Gnomad4 ASJ

AF:

0.0898

Gnomad4 EAS

AF:

0.0645

Gnomad4 SAS

AF:

0.139

Gnomad4 FIN

AF:

0.0886

Gnomad4 NFE

AF:

0.0713

Gnomad4 OTH

AF:

0.145

Alfa

AF:

0.0305

Hom.:

Bravo

AF:

0.173

Asia WGS

AF:

0.112

AC:

392

AN:

3478

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

GeneDx

Aug 20, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.85

CADD

Benign

3.4

DANN

Benign

0.68

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