Variant 5-151673098-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_003118.4(SPARC):c.208+31C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.598 in 1,533,806 control chromosomes in the GnomAD database, including 277,194 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.65 ( 32418 hom., cov: 33)

Exomes 𝑓: 0.59 ( 244776 hom. )

Consequence

SPARC
NM_003118.4 intron

Scores

Clinical Significance

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

Conservation

PhyloP100: -0.0850

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 -20 ACMG points.

BP4

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

BP6

Variant 5-151673098-G-A is Benign according to our data. Variant chr5-151673098-G-A is described in ClinVar as [Benign]. Clinvar id is 1278457.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.768 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	MANE	Protein
SPARC	NM_003118.4 linkuse as main transcript	c.208+31C>T	intron_variant	ENST00000231061.9	NP_003109.1
SPARC	NM_001309443.2 linkuse as main transcript	c.205+31C>T	intron_variant		NP_001296372.1
SPARC	NM_001309444.2 linkuse as main transcript	c.208+31C>T	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.208+31C>T		intron_variant		1	NM_003118.4	ENSP00000231061	P1

Frequencies

GnomAD3 genomes

AF:

0.646

AC:

98276

AN:

152022

Hom.:

32374

Cov.:

show subpopulations

Gnomad AFR

AF:

0.775

Gnomad AMI

AF:

0.662

Gnomad AMR

AF:

0.649

Gnomad ASJ

AF:

0.591

Gnomad EAS

AF:

0.512

Gnomad SAS

AF:

0.541

Gnomad FIN

AF:

0.655

Gnomad MID

AF:

0.604

Gnomad NFE

AF:

0.587

Gnomad OTH

AF:

0.633

GnomAD3 exomes

AF:

0.605

AC:

151939

AN:

251256

Hom.:

46558

AF XY:

0.596

AC XY:

80942

AN XY:

135778

show subpopulations

Gnomad AFR exome

AF:

0.783

Gnomad AMR exome

AF:

0.663

Gnomad ASJ exome

AF:

0.592

Gnomad EAS exome

AF:

0.501

Gnomad SAS exome

AF:

0.547

Gnomad FIN exome

AF:

0.647

Gnomad NFE exome

AF:

0.587

Gnomad OTH exome

AF:

0.598

GnomAD4 exome

AF:

0.593

AC:

818919

AN:

1381664

Hom.:

244776

Cov.:

AF XY:

0.589

AC XY:

408102

AN XY:

692384

show subpopulations

Gnomad4 AFR exome

AF:

0.788

Gnomad4 AMR exome

AF:

0.657

Gnomad4 ASJ exome

AF:

0.586

Gnomad4 EAS exome

AF:

0.534

Gnomad4 SAS exome

AF:

0.543

Gnomad4 FIN exome

AF:

0.647

Gnomad4 NFE exome

AF:

0.588

Gnomad4 OTH exome

AF:

0.590

GnomAD4 genome

AF:

0.647

AC:

98376

AN:

152142

Hom.:

32418

Cov.:

AF XY:

0.648

AC XY:

48193

AN XY:

74378

show subpopulations

Gnomad4 AFR

AF:

0.775

Gnomad4 AMR

AF:

0.649

Gnomad4 ASJ

AF:

0.591

Gnomad4 EAS

AF:

0.512

Gnomad4 SAS

AF:

0.542

Gnomad4 FIN

AF:

0.655

Gnomad4 NFE

AF:

0.587

Gnomad4 OTH

AF:

0.638

Alfa

AF:

0.613

Hom.:

5919

Bravo

AF:

0.652

Asia WGS

AF:

0.578

AC:

2013

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

Osteogenesis imperfecta type 17

Benign:1

Benign, criteria provided, single submitter

clinical testing

Genome-Nilou Lab

Jul 15, 2021

- -

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Aug 09, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.79

CADD

Benign

2.6

DANN

Benign

0.77

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