NM_001034852.3:c.83G>A

Variant names:

• chr14-69879761-G-A
• NM_001034852.3:c.83G>A

Variant summary

Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2 BP4

The NM_001034852.3(SMOC1):​c.83G>A​(p.Arg28His) variant causes a missense change. The variant allele was found at a frequency of 0.000000695 in 1,438,852 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: not found (cov: 33)
  • Exomes 𝑓: 6.9e-7 (0 hom.)
• Consequence: SMOC1 NM_001034852.3 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 4.92

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]

ACMG classification

Verdict is Uncertain_significance. Variant got 1 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.30094695).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SMOC1	NM_001034852.3	c.83G>A	p.Arg28His	missense_variant	Exon 1 of 12	ENST00000361956.8	NP_001030024.1
SMOC1	NM_001425244.1	c.83G>A	p.Arg28His	missense_variant	Exon 1 of 12		NP_001412173.1
SMOC1	NM_001425245.1	c.83G>A	p.Arg28His	missense_variant	Exon 1 of 12		NP_001412174.1
SMOC1	NM_022137.6	c.83G>A	p.Arg28His	missense_variant	Exon 1 of 12		NP_071420.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SMOC1	ENST00000361956.8	c.83G>A	p.Arg28His	missense_variant	Exon 1 of 12	1	NM_001034852.3	ENSP00000355110.4
SMOC1	ENST00000381280.4	c.83G>A	p.Arg28His	missense_variant	Exon 1 of 12	1		ENSP00000370680.4
SMOC1	ENST00000555917.1	n.404+15547G>A		intron_variant	Intron 3 of 3	4

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome AF: 6.95e-7 AC: 1 AN: 1438852 Hom.: 0 Cov.: 31 AF XY: 0.00000140 AC XY: 1 AN XY: 715590

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.0000257

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.00

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome Cov.: 33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.15
BayesDel_addAF	Benign	-0.059	T
BayesDel_noAF	Benign	-0.32
CADD	Pathogenic	26
DANN	Uncertain	1.0
DEOGEN2	Benign	0.15	.;T
Eigen	Benign	0.14
Eigen_PC	Benign	0.22
FATHMM_MKL	Uncertain	0.88	D
LIST_S2	Uncertain	0.89	D;D
M_CAP	Uncertain	0.19	D
MetaRNN	Benign	0.30	T;T
MetaSVM	Benign	-0.80	T
MutationAssessor	Benign	0.34	N;N
PrimateAI	Pathogenic	0.88	D
PROVEAN	Benign	-1.7	N;N
REVEL	Benign	0.16
Sift	Benign	0.15	T;T
Sift4G	Benign	0.072	T;T
Polyphen		0.94	P;P
Vest4		0.28
MutPred		0.38		Loss of methylation at R28 (P = 0.0163);Loss of methylation at R28 (P = 0.0163);
MVP		0.73
MPC		0.55
ClinPred		0.92	D
GERP RS		5.0
Varity_R		0.20
gMVP		0.17

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

No publications associated with this variant yet.

Other links and lift over

hg19: chr14-70346478;