rs370866589

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2

The NM_001034852.3(SMOC1):ā€‹c.223C>Gā€‹(p.Arg75Gly) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000558 in 1,614,066 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: š‘“ 0.0000066 ( 0 hom., cov: 32)
Exomes š‘“: 0.0000055 ( 0 hom. )

Consequence

SMOC1
NM_001034852.3 missense

Scores

10
9

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.22
Variant links:
Genes affected
SMOC1 (HGNC:20318): (SPARC related modular calcium binding 1) This gene encodes a multi-domain secreted protein that may have a critical role in ocular and limb development. Mutations in this gene are associated with microphthalmia and limb anomalies. Alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Mar 2011]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 2 ACMG points.

PM2
Very rare variant in population databases, with high coverage;

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
SMOC1NM_001034852.3 linkc.223C>G p.Arg75Gly missense_variant Exon 2 of 12 ENST00000361956.8 NP_001030024.1 Q9H4F8-2
SMOC1NM_001425244.1 linkc.223C>G p.Arg75Gly missense_variant Exon 2 of 12 NP_001412173.1
SMOC1NM_001425245.1 linkc.223C>G p.Arg75Gly missense_variant Exon 2 of 12 NP_001412174.1
SMOC1NM_022137.6 linkc.223C>G p.Arg75Gly missense_variant Exon 2 of 12 NP_071420.1 Q9H4F8-1A0A024R6E0

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
SMOC1ENST00000361956.8 linkc.223C>G p.Arg75Gly missense_variant Exon 2 of 12 1 NM_001034852.3 ENSP00000355110.4 Q9H4F8-2
SMOC1ENST00000381280.4 linkc.223C>G p.Arg75Gly missense_variant Exon 2 of 12 1 ENSP00000370680.4 Q9H4F8-1
SMOC1ENST00000553839.1 linkn.125C>G non_coding_transcript_exon_variant Exon 1 of 4 5
SMOC1ENST00000555917.1 linkn.528C>G non_coding_transcript_exon_variant Exon 4 of 4 4

Frequencies

GnomAD3 genomes
AF:
0.00000657
AC:
1
AN:
152194
Hom.:
0
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.00
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00
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:
0.0000147
Gnomad OTH
AF:
0.00
GnomAD3 exomes
AF:
0.00000398
AC:
1
AN:
251332
Hom.:
0
AF XY:
0.00000736
AC XY:
1
AN XY:
135820
show subpopulations
Gnomad AFR exome
AF:
0.00
Gnomad AMR exome
AF:
0.00
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.00
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.00000880
Gnomad OTH exome
AF:
0.00
GnomAD4 exome
AF:
0.00000547
AC:
8
AN:
1461872
Hom.:
0
Cov.:
33
AF XY:
0.00000275
AC XY:
2
AN XY:
727242
show subpopulations
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.00
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.00000719
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
AF:
0.00000657
AC:
1
AN:
152194
Hom.:
0
Cov.:
32
AF XY:
0.0000134
AC XY:
1
AN XY:
74352
show subpopulations
Gnomad4 AFR
AF:
0.00
Gnomad4 AMR
AF:
0.00
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.0000147
Gnomad4 OTH
AF:
0.00
Alfa
AF:
0.0000278
Hom.:
0
Bravo
AF:
0.00000756
ExAC
AF:
0.00000824
AC:
1

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Uncertain
0.37
BayesDel_addAF
Benign
-0.097
T
BayesDel_noAF
Benign
-0.38
CADD
Benign
23
DANN
Uncertain
1.0
DEOGEN2
Benign
0.21
.;T
Eigen
Benign
0.15
Eigen_PC
Benign
0.10
FATHMM_MKL
Uncertain
0.85
D
LIST_S2
Uncertain
0.92
D;D
M_CAP
Benign
0.018
T
MetaRNN
Uncertain
0.68
D;D
MetaSVM
Benign
-1.0
T
MutationAssessor
Uncertain
2.8
M;M
PrimateAI
Uncertain
0.58
T
PROVEAN
Uncertain
-3.8
D;D
REVEL
Benign
0.17
Sift
Uncertain
0.0040
D;D
Sift4G
Uncertain
0.0070
D;D
Polyphen
0.88
P;P
Vest4
0.71
MutPred
0.55
Loss of MoRF binding (P = 0.0208);Loss of MoRF binding (P = 0.0208);
MVP
0.30
MPC
0.90
ClinPred
0.98
D
GERP RS
0.67
Varity_R
0.45
gMVP
0.32

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.030
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: rs370866589; hg19: chr14-70418978; API