6-168672861-C-T

Variant names:

• chr6-168672861-C-T
• rs196450
• ENST00000477998.1:n.130-352C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000477998.1(SMOC2):​n.130-352C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.425 in 151,976 control chromosomes in the GnomAD database, including 16,384 homozygotes. 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: 𝑓 0.42 (16384 hom., cov: 32)
• Consequence: SMOC2 ENST00000477998.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.84
• Publications: 0 publications found

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]

SMOC2 Gene-Disease associations (from GenCC):

• dentin dysplasia type I

  Inheritance: AR Classification: STRONG, LIMITED Submitted by: Ambry Genetics, G2P, Labcorp Genetics (formerly Invitae)
• atypical dentin dysplasia due to SMOC2 deficiency

  Inheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet

LOC124901467 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.569 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124901467	XR_007059885.1	n.195-352C>T		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SMOC2	ENST00000477998.1	n.130-352C>T		intron_variant	Intron 3 of 3	3

Frequencies

GnomAD3 genomes AF: 0.425 AC: 64599 AN: 151858 Hom.: 16400 Cov.: 32

Gnomad AFR AF: 0.135

Gnomad AMI AF: 0.668

Gnomad AMR AF: 0.443

Gnomad ASJ AF: 0.525

Gnomad EAS AF: 0.324

Gnomad SAS AF: 0.480

Gnomad FIN AF: 0.543

Gnomad MID AF: 0.516

Gnomad NFE AF: 0.573

Gnomad OTH AF: 0.467

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.425 AC: 64574 AN: 151976 Hom.: 16384 Cov.: 32 AF XY: 0.425 AC XY: 31552 AN XY: 74276

African (AFR) AF: 0.135 AC: 5603 AN: 41466

American (AMR) AF: 0.443 AC: 6759 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.525 AC: 1822 AN: 3470

East Asian (EAS) AF: 0.323 AC: 1663 AN: 5144

South Asian (SAS) AF: 0.479 AC: 2303 AN: 4806

European-Finnish (FIN) AF: 0.543 AC: 5718 AN: 10536

Middle Eastern (MID) AF: 0.517 AC: 151 AN: 292

European-Non Finnish (NFE) AF: 0.573 AC: 38976 AN: 67968

Other (OTH) AF: 0.460 AC: 971 AN: 2112

Alfa AF: 0.477 Hom.: 2568

Bravo AF: 0.404

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.034
PhyloP100		-2.8

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs196450; hg19: chr6-169073400;