Variant 5-151663542-G-C 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.*29C>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.162 in 1,605,196 control chromosomes in the GnomAD database, including 25,389 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.17 ( 2608 hom., cov: 33)

Exomes 𝑓: 0.16 ( 22781 hom. )

Consequence

SPARC
NM_003118.4 3_prime_UTR

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.373

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=-0.75).

BP6

Variant 5-151663542-G-C is Benign according to our data. Variant chr5-151663542-G-C is described in ClinVar as [Benign]. Clinvar id is 1272922.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.367 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE
SPARC	NM_003118.4 linkuse as main transcript	c.*29C>G		3_prime_UTR_variant	10/10	ENST00000231061.9
SPARC	NM_001309444.2 linkuse as main transcript	c.939C>G	p.Leu313=	synonymous_variant	10/10
SPARC	NM_001309443.2 linkuse as main transcript	c.*29C>G		3_prime_UTR_variant	10/10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SPARC	ENST00000231061.9 linkuse as main transcript	c.*29C>G		3_prime_UTR_variant	10/10	1	NM_003118.4	P1
SPARC	ENST00000520687.1 linkuse as main transcript	n.544C>G		non_coding_transcript_exon_variant	4/4	2

Frequencies

GnomAD3 genomes

AF:

0.172

AC:

26175

AN:

152092

Hom.:

2606

Cov.:

show subpopulations

Gnomad AFR

AF:

0.150

Gnomad AMI

AF:

0.121

Gnomad AMR

AF:

0.299

Gnomad ASJ

AF:

0.160

Gnomad EAS

AF:

0.381

Gnomad SAS

AF:

0.223

Gnomad FIN

AF:

0.148

Gnomad MID

AF:

0.244

Gnomad NFE

AF:

0.142

Gnomad OTH

AF:

0.183

GnomAD3 exomes

AF:

0.211

AC:

52435

AN:

248960

Hom.:

7272

AF XY:

0.202

AC XY:

27225

AN XY:

134764

show subpopulations

Gnomad AFR exome

AF:

0.149

Gnomad AMR exome

AF:

0.426

Gnomad ASJ exome

AF:

0.164

Gnomad EAS exome

AF:

0.373

Gnomad SAS exome

AF:

0.218

Gnomad FIN exome

AF:

0.148

Gnomad NFE exome

AF:

0.142

Gnomad OTH exome

AF:

0.189

GnomAD4 exome

AF:

0.161

AC:

233765

AN:

1452986

Hom.:

22781

Cov.:

AF XY:

0.162

AC XY:

116912

AN XY:

723362

show subpopulations

Gnomad4 AFR exome

AF:

0.149

Gnomad4 AMR exome

AF:

0.409

Gnomad4 ASJ exome

AF:

0.166

Gnomad4 EAS exome

AF:

0.412

Gnomad4 SAS exome

AF:

0.218

Gnomad4 FIN exome

AF:

0.152

Gnomad4 NFE exome

AF:

0.138

Gnomad4 OTH exome

AF:

0.168

GnomAD4 genome

AF:

0.172

AC:

26194

AN:

152210

Hom.:

2608

Cov.:

AF XY:

0.177

AC XY:

13174

AN XY:

74408

show subpopulations

Gnomad4 AFR

AF:

0.149

Gnomad4 AMR

AF:

0.300

Gnomad4 ASJ

AF:

0.160

Gnomad4 EAS

AF:

0.381

Gnomad4 SAS

AF:

0.223

Gnomad4 FIN

AF:

0.148

Gnomad4 NFE

AF:

0.142

Gnomad4 OTH

AF:

0.185

Alfa

AF:

0.161

Hom.:

392

Bravo

AF:

0.181

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

-0.75

CADD

Benign

DANN

Benign

0.70

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

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