chr3-8766742-G-GC

Position:

• chr3-8766742-G-GC

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1

The NM_000916.4(OXTR):​c.922+523dupG variant causes a intron change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.63 (30485 hom., cov: 0)
• Consequence: OXTR NM_000916.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00600

Genes affected

OXTR (HGNC:8529): (oxytocin receptor) The protein encoded by this gene belongs to the G-protein coupled receptor family and acts as a receptor for oxytocin. Its activity is mediated by G proteins which activate a phosphatidylinositol-calcium second messenger system. The oxytocin-oxytocin receptor system plays an important role in the uterus during parturition. [provided by RefSeq, Jul 2008]

CAV3 (HGNC:1529): (caveolin 3) This gene encodes a caveolin family member, which functions as a component of the caveolae plasma membranes found in most cell types. Caveolin proteins are proposed to be scaffolding proteins for organizing and concentrating certain caveolin-interacting molecules. Mutations identified in this gene lead to interference with protein oligomerization or intra-cellular routing, disrupting caveolae formation and resulting in Limb-Girdle muscular dystrophy type-1C (LGMD-1C), hyperCKemia or rippling muscle disease (RMD). Alternative splicing has been identified for this locus, with inclusion or exclusion of a differentially spliced intron. In addition, transcripts utilize multiple polyA sites and contain two potential translation initiation sites. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -8 ACMG points.

• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.755 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
OXTR	NM_000916.4	c.922+523dupG		intron_variant		ENST00000316793.8	NP_000907.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
OXTR	ENST00000316793.8	c.922+523_922+524insG		intron_variant		1	NM_000916.4	ENSP00000324270.2
CAV3	ENST00000472766.1	n.156-10735_156-10734insC		intron_variant		2

Frequencies

GnomAD3 genomes AF: 0.626 AC: 94796 AN: 151496 Hom.: 30452 Cov.: 0

Gnomad AFR AF: 0.762

Gnomad AMI AF: 0.637

Gnomad AMR AF: 0.628

Gnomad ASJ AF: 0.589

Gnomad EAS AF: 0.309

Gnomad SAS AF: 0.555

Gnomad FIN AF: 0.441

Gnomad MID AF: 0.595

Gnomad NFE AF: 0.602

Gnomad OTH AF: 0.618

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

GnomAD4 genome AF: 0.626 AC: 94885 AN: 151612 Hom.: 30485 Cov.: 0 AF XY: 0.615 AC XY: 45545 AN XY: 74110

Gnomad4 AFR AF: 0.762

Gnomad4 AMR AF: 0.628

Gnomad4 ASJ AF: 0.589

Gnomad4 EAS AF: 0.309

Gnomad4 SAS AF: 0.555

Gnomad4 FIN AF: 0.441

Gnomad4 NFE AF: 0.602

Gnomad4 OTH AF: 0.619

Alfa AF: 0.614 Hom.: 3105

Bravo AF: 0.644

Asia WGS AF: 0.479 AC: 1663 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Other links and lift over

dbSNP: rs3831817; hg19: chr3-8808428;