5-173325979-G-C

Variant names:

• chr5-173325979-G-C
• rs114346665
• NM_003714.3:c.183C>G

Variant summary

Our verdict is Likely benign. The variant received -1 ACMG points: 2P and 3B. PM2 BP4_Moderate BP7

The NM_003714.3(STC2):​c.183C>G​(p.Gly61Gly) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Synonymous variant affecting the same amino acid position (i.e. G61G) has been classified as Benign.

• Frequency: Genomes: not found (cov: 33)
• Consequence: STC2 NM_003714.3 synonymous
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.185
• Publications: 0 publications found

Genes affected

STC2 (HGNC:11374): (stanniocalcin 2) This gene encodes a secreted, homodimeric glycoprotein that is expressed in a wide variety of tissues and may have autocrine or paracrine functions. The encoded protein has 10 of its 15 cysteine residues conserved among stanniocalcin family members and is phosphorylated by casein kinase 2 exclusively on its serine residues. Its C-terminus contains a cluster of histidine residues which may interact with metal ions. The protein may play a role in the regulation of renal and intestinal calcium and phosphate transport, cell metabolism, or cellular calcium/phosphate homeostasis. Constitutive overexpression of human stanniocalcin 2 in mice resulted in pre- and postnatal growth restriction, reduced bone and skeletal muscle growth, and organomegaly. Expression of this gene is induced by estrogen and altered in some breast cancers. [provided by RefSeq, Jul 2008]

ACMG classification

Our verdict: Likely_benign. The variant received -1 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (REVEL=0.084).
• BP7: Synonymous conserved (PhyloP=-0.185 with no splicing effect.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_003714.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	STC2	NM_003714.3	MANE Select	c.183C>G	p.Gly61Gly	synonymous	Exon 2 of 4	NP_003705.1	O76061

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	STC2	ENST00000265087.9	TSL:1 MANE Select	c.183C>G	p.Gly61Gly	synonymous	Exon 2 of 4	ENSP00000265087.4	O76061
	STC2	ENST00000520648.1	TSL:2	c.42C>G	p.Gly14Gly	synonymous	Exon 2 of 3	ENSP00000428470.1	H0YB13
	STC2	ENST00000518455.1	TSL:5	c.-73C>G		5_prime_UTR	Exon 2 of 3	ENSP00000427816.1	E5RG57

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Cov.: 31

GnomAD4 genome Cov.: 33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.51
CADD	Benign	5.2
DANN	Benign	0.74
PhyloP100		-0.18

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.10		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs114346665; hg19: chr5-172752982;