Variant rs729853 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.585+100G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.165 in 1,397,492 control chromosomes in the GnomAD database, including 23,145 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.17 ( 2625 hom., cov: 32)

Exomes 𝑓: 0.16 ( 20520 hom. )

Consequence

SPARC
NM_003118.4 intron

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.937

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:

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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=-0.82).

BP6

Variant 5-151667367-C-T is Benign according to our data. Variant chr5-151667367-C-T is described in ClinVar as [Benign]. Clinvar id is 1237216.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.366 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	MANE	Protein
SPARC	NM_003118.4 linkuse as main transcript	c.585+100G>A	intron_variant	ENST00000231061.9	NP_003109.1
SPARC	NM_001309443.2 linkuse as main transcript	c.582+100G>A	intron_variant		NP_001296372.1
SPARC	NM_001309444.2 linkuse as main transcript	c.585+100G>A	intron_variant		NP_001296373.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SPARC	ENST00000231061.9 linkuse as main transcript	c.585+100G>A		intron_variant		1	NM_003118.4	ENSP00000231061	P1

Frequencies

GnomAD3 genomes

AF:

0.173

AC:

26236

AN:

152036

Hom.:

2623

Cov.:

show subpopulations

Gnomad AFR

AF:

0.150

Gnomad AMI

AF:

0.121

Gnomad AMR

AF:

0.299

Gnomad ASJ

AF:

0.161

Gnomad EAS

AF:

0.379

Gnomad SAS

AF:

0.222

Gnomad FIN

AF:

0.149

Gnomad MID

AF:

0.244

Gnomad NFE

AF:

0.143

Gnomad OTH

AF:

0.181

GnomAD4 exome

AF:

0.164

AC:

204343

AN:

1245336

Hom.:

20520

AF XY:

0.164

AC XY:

103134

AN XY:

627058

show subpopulations

Gnomad4 AFR exome

AF:

0.149

Gnomad4 AMR exome

AF:

0.410

Gnomad4 ASJ exome

AF:

0.166

Gnomad4 EAS exome

AF:

0.410

Gnomad4 SAS exome

AF:

0.218

Gnomad4 FIN exome

AF:

0.152

Gnomad4 NFE exome

AF:

0.139

Gnomad4 OTH exome

AF:

0.169

GnomAD4 genome

AF:

0.173

AC:

26255

AN:

152156

Hom.:

2625

Cov.:

AF XY:

0.177

AC XY:

13201

AN XY:

74380

show subpopulations

Gnomad4 AFR

AF:

0.149

Gnomad4 AMR

AF:

0.300

Gnomad4 ASJ

AF:

0.161

Gnomad4 EAS

AF:

0.380

Gnomad4 SAS

AF:

0.222

Gnomad4 FIN

AF:

0.149

Gnomad4 NFE

AF:

0.143

Gnomad4 OTH

AF:

0.184

Alfa

AF:

0.154

Hom.:

3562

Bravo

AF:

0.182

Asia WGS

AF:

0.302

AC:

1047

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 25, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.82

CADD

Benign

1.2

DANN

Benign

0.73

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