chr10-72067017-G-A
Variant summary
Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BS1BS2
The NM_001244950.2(SPOCK2):c.813C>T(p.Ala271=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00144 in 1,614,212 control chromosomes in the GnomAD database, including 29 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.0078 ( 16 hom., cov: 32)
Exomes 𝑓: 0.00078 ( 13 hom. )
Consequence
SPOCK2
NM_001244950.2 synonymous
NM_001244950.2 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -4.13
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]
Genome browser will be placed here
ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -15 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.78).
BP6
?
Variant 10-72067017-G-A is Benign according to our data. Variant chr10-72067017-G-A is described in ClinVar as [Benign]. Clinvar id is 780138.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=-4.13 with no splicing effect.
BS1
?
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.0078 (1188/152338) while in subpopulation AFR AF= 0.0262 (1090/41570). AF 95% confidence interval is 0.0249. There are 16 homozygotes in gnomad4. There are 513 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
?
High Homozygotes in GnomAd at 16 gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SPOCK2 | NM_001244950.2 | c.813C>T | p.Ala271= | synonymous_variant | 8/11 | ENST00000373109.7 | |
SPOCK2 | NM_014767.2 | c.813C>T | p.Ala271= | synonymous_variant | 9/12 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SPOCK2 | ENST00000373109.7 | c.813C>T | p.Ala271= | synonymous_variant | 8/11 | 1 | NM_001244950.2 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00779 AC: 1186AN: 152220Hom.: 16 Cov.: 32
GnomAD3 genomes
?
AF:
AC:
1186
AN:
152220
Hom.:
Cov.:
32
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD3 exomes AF: 0.00198 AC: 498AN: 251452Hom.: 3 AF XY: 0.00146 AC XY: 198AN XY: 135902
GnomAD3 exomes
AF:
AC:
498
AN:
251452
Hom.:
AF XY:
AC XY:
198
AN XY:
135902
Gnomad AFR exome
AF:
Gnomad AMR exome
AF:
Gnomad ASJ exome
AF:
Gnomad EAS exome
AF:
Gnomad SAS exome
AF:
Gnomad FIN exome
AF:
Gnomad NFE exome
AF:
Gnomad OTH exome
AF:
GnomAD4 exome AF: 0.000775 AC: 1133AN: 1461874Hom.: 13 Cov.: 32 AF XY: 0.000677 AC XY: 492AN XY: 727240
GnomAD4 exome
AF:
AC:
1133
AN:
1461874
Hom.:
Cov.:
32
AF XY:
AC XY:
492
AN XY:
727240
Gnomad4 AFR exome
AF:
Gnomad4 AMR exome
AF:
Gnomad4 ASJ exome
AF:
Gnomad4 EAS exome
AF:
Gnomad4 SAS exome
AF:
Gnomad4 FIN exome
AF:
Gnomad4 NFE exome
AF:
Gnomad4 OTH exome
AF:
GnomAD4 genome ? AF: 0.00780 AC: 1188AN: 152338Hom.: 16 Cov.: 32 AF XY: 0.00689 AC XY: 513AN XY: 74492
GnomAD4 genome
?
AF:
AC:
1188
AN:
152338
Hom.:
Cov.:
32
AF XY:
AC XY:
513
AN XY:
74492
Gnomad4 AFR
AF:
Gnomad4 AMR
AF:
Gnomad4 ASJ
AF:
Gnomad4 EAS
AF:
Gnomad4 SAS
AF:
Gnomad4 FIN
AF:
Gnomad4 NFE
AF:
Gnomad4 OTH
AF:
Alfa
AF:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
8
AN:
3478
EpiCase
AF:
EpiControl
AF:
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 | Invitae | Dec 31, 2019 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at