6-168441267-C-T

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1

The NM_001166412.2(SMOC2):​c.-104C>T variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0827 in 1,375,156 control chromosomes in the GnomAD database, including 5,133 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.065 ( 383 hom., cov: 33)
Exomes 𝑓: 0.085 ( 4750 hom. )

Consequence

SMOC2
NM_001166412.2 5_prime_UTR

Scores

2

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.0620
Variant links:
Genes affected
SMOC2 (HGNC:20323): (SPARC related modular calcium binding 2) This gene encodes a member of the SPARC family (secreted protein acidic and rich in cysteine/osteonectin/BM-40), which are highly expressed during embryogenesis and wound healing. The gene product is a matricellular protein which promotes matrix assembly and can stimulate endothelial cell proliferation and migration, as well as angiogenic activity. Associated with pulmonary function, this secretory gene product contains a Kazal domain, two thymoglobulin type-1 domains, and two EF-hand calcium-binding domains. The encoded protein may serve as a target for controlling angiogenesis in tumor growth and myocardial ischemia. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Oct 2009]

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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=-0.66).
BP6
Variant 6-168441267-C-T is Benign according to our data. Variant chr6-168441267-C-T is described in ClinVar as [Benign]. Clinvar id is 1273584.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.091 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
SMOC2NM_001166412.2 linkc.-104C>T 5_prime_UTR_variant Exon 1 of 13 ENST00000356284.7 NP_001159884.1 Q9H3U7-1
SMOC2NM_022138.3 linkc.-104C>T 5_prime_UTR_variant Exon 1 of 13 NP_071421.1 Q9H3U7-2
SMOC2XM_011536065.2 linkc.-104C>T 5_prime_UTR_variant Exon 1 of 13 XP_011534367.1
SMOC2XM_011536066.2 linkc.-104C>T 5_prime_UTR_variant Exon 1 of 13 XP_011534368.1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
SMOC2ENST00000356284 linkc.-104C>T 5_prime_UTR_variant Exon 1 of 13 1 NM_001166412.2 ENSP00000348630.3 Q9H3U7-1
SMOC2ENST00000354536 linkc.-104C>T 5_prime_UTR_variant Exon 1 of 13 1 ENSP00000346537.5 Q9H3U7-2

Frequencies

GnomAD3 genomes
AF:
0.0648
AC:
9856
AN:
152058
Hom.:
384
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.0315
Gnomad AMI
AF:
0.173
Gnomad AMR
AF:
0.0425
Gnomad ASJ
AF:
0.0599
Gnomad EAS
AF:
0.00271
Gnomad SAS
AF:
0.0561
Gnomad FIN
AF:
0.0746
Gnomad MID
AF:
0.0573
Gnomad NFE
AF:
0.0930
Gnomad OTH
AF:
0.0578
GnomAD4 exome
AF:
0.0850
AC:
103895
AN:
1222990
Hom.:
4750
Cov.:
29
AF XY:
0.0843
AC XY:
50069
AN XY:
594226
show subpopulations
Gnomad4 AFR exome
AF:
0.0302
Gnomad4 AMR exome
AF:
0.0370
Gnomad4 ASJ exome
AF:
0.0606
Gnomad4 EAS exome
AF:
0.000560
Gnomad4 SAS exome
AF:
0.0632
Gnomad4 FIN exome
AF:
0.0792
Gnomad4 NFE exome
AF:
0.0916
Gnomad4 OTH exome
AF:
0.0713
GnomAD4 genome
AF:
0.0647
AC:
9851
AN:
152166
Hom.:
383
Cov.:
33
AF XY:
0.0631
AC XY:
4692
AN XY:
74388
show subpopulations
Gnomad4 AFR
AF:
0.0315
Gnomad4 AMR
AF:
0.0425
Gnomad4 ASJ
AF:
0.0599
Gnomad4 EAS
AF:
0.00272
Gnomad4 SAS
AF:
0.0557
Gnomad4 FIN
AF:
0.0746
Gnomad4 NFE
AF:
0.0930
Gnomad4 OTH
AF:
0.0573
Alfa
AF:
0.0740
Hom.:
59
Bravo
AF:
0.0597
Asia WGS
AF:
0.0420
AC:
145
AN:
3460

ClinVar

Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not provided Benign:1
Jun 19, 2021
GeneDx
Significance: Benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing

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Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.66
CADD
Benign
5.8
DANN
Benign
0.96
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
1.0

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.

Other links and lift over

dbSNP: rs143067962; hg19: chr6-168841947; API