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GeneBe

10-72062886-C-T

Variant summary

Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2

The NM_001244950.2(SPOCK2):c.1149G>A(p.Ser383=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000643 in 1,599,432 control chromosomes in the GnomAD database, including 10 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.0034 ( 9 hom., cov: 31)
Exomes 𝑓: 0.00036 ( 1 hom. )

Consequence

SPOCK2
NM_001244950.2 synonymous

Scores

2

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -6.95
Variant links:
Genes affected
SPOCK2 (HGNC:13564): (SPARC (osteonectin), cwcv and kazal like domains proteoglycan 2) This gene encodes a protein which binds with glycosaminoglycans to form part of the extracellular matrix. The protein contains thyroglobulin type-1, follistatin-like, and calcium-binding domains, and has glycosaminoglycan attachment sites in the acidic C-terminal region. Three alternatively spliced transcript variants that encode different protein isoforms have been described for this gene. [provided by RefSeq, Oct 2011]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -11 ACMG points.

BP4
?
    BP4 - Multiple lines of computational evidence suggest no impact on gene or gene product (conservation, evolutionary, splicing impact, etc.)
Computational evidence support a benign effect (BayesDel_noAF=-0.71).
BP6
?
    BP6 - Reputable source recently reports variant as benign, but the evidence is not available to the laboratory to perform an independent evaluation
Variant 10-72062886-C-T is Benign according to our data. Variant chr10-72062886-C-T is described in ClinVar as [Benign]. Clinvar id is 768372.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
    BP7 - A synonymous (silent) variant for which splicing prediction algorithms predict no impact to the splice consensus sequence nor the creation of a new splice site AND the nucleotide is not highly conserved
Synonymous conserved (PhyloP=-6.95 with no splicing effect.
BS2
?
    BS2 - Observed in a healthy adult individual for a recessive (homozygous), dominant (heterozygous), or X-linked (hemizygous) disorder, with full penetrance expected at an early age
High Homozygotes in GnomAd at 9 gene

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
SPOCK2NM_001244950.2 linkuse as main transcriptc.1149G>A p.Ser383= synonymous_variant 11/11 ENST00000373109.7
SPOCK2NM_014767.2 linkuse as main transcriptc.1149G>A p.Ser383= synonymous_variant 12/12

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
SPOCK2ENST00000373109.7 linkuse as main transcriptc.1149G>A p.Ser383= synonymous_variant 11/111 NM_001244950.2 P1Q92563-1
SPOCK2ENST00000317376.8 linkuse as main transcriptc.1149G>A p.Ser383= synonymous_variant 12/121 P1Q92563-1
SPOCK2ENST00000463279.6 linkuse as main transcriptn.717G>A non_coding_transcript_exon_variant 7/75
SPOCK2ENST00000469121.5 linkuse as main transcriptn.785G>A non_coding_transcript_exon_variant 7/73

Frequencies

GnomAD3 genomes
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.00337
AC:
513
AN:
152110
Hom.:
9
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.0118
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.000916
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.0000735
Gnomad OTH
AF:
0.00287
GnomAD3 exomes
AF:
0.000874
AC:
199
AN:
227750
Hom.:
0
AF XY:
0.000641
AC XY:
79
AN XY:
123238
show subpopulations
Gnomad AFR exome
AF:
0.0120
Gnomad AMR exome
AF:
0.000554
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.0000349
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.0000784
Gnomad OTH exome
AF:
0.00
GnomAD4 exome
AF:
0.000357
AC:
517
AN:
1447204
Hom.:
1
Cov.:
76
AF XY:
0.000335
AC XY:
241
AN XY:
719172
show subpopulations
Gnomad4 AFR exome
AF:
0.0106
Gnomad4 AMR exome
AF:
0.000556
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.0000236
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.0000831
Gnomad4 OTH exome
AF:
0.000750
GnomAD4 genome
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.00336
AC:
512
AN:
152228
Hom.:
9
Cov.:
31
AF XY:
0.00304
AC XY:
226
AN XY:
74408
show subpopulations
Gnomad4 AFR
AF:
0.0117
Gnomad4 AMR
AF:
0.000915
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.0000735
Gnomad4 OTH
AF:
0.00284
Alfa
AF:
0.00167
Hom.:
1
Bravo
AF:
0.00385
Asia WGS
AF:
0.000289
AC:
1
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 submitterclinical testingInvitaeApr 16, 2018- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.71
Cadd
Benign
0.40
Dann
Benign
0.54

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.11
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.

Other links and lift over

dbSNP: rs115217058; hg19: chr10-73822644; COSMIC: COSV58038062; COSMIC: COSV58038062; API