chr3-8758986-C-T

Position:

• chr3-8758986-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_000916.4(OXTR):​c.923-5762G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.244 in 152,188 control chromosomes in the GnomAD database, including 5,403 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 0.24 (5403 hom., cov: 33)
• Consequence: OXTR NM_000916.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.821

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 -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.301 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
OXTR	NM_000916.4	c.923-5762G>A		intron_variant		ENST00000316793.8	NP_000907.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
OXTR	ENST00000316793.8	c.923-5762G>A		intron_variant		1	NM_000916.4	ENSP00000324270.2
CAV3	ENST00000472766.1	n.156-18491C>T		intron_variant		2

Frequencies

GnomAD3 genomes AF: 0.244 AC: 37114 AN: 152070 Hom.: 5398 Cov.: 33

Gnomad AFR AF: 0.105

Gnomad AMI AF: 0.433

Gnomad AMR AF: 0.308

Gnomad ASJ AF: 0.215

Gnomad EAS AF: 0.139

Gnomad SAS AF: 0.177

Gnomad FIN AF: 0.404

Gnomad MID AF: 0.180

Gnomad NFE AF: 0.302

Gnomad OTH AF: 0.239

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

GnomAD4 genome AF: 0.244 AC: 37142 AN: 152188 Hom.: 5403 Cov.: 33 AF XY: 0.246 AC XY: 18270 AN XY: 74386

Gnomad4 AFR AF: 0.105

Gnomad4 AMR AF: 0.309

Gnomad4 ASJ AF: 0.215

Gnomad4 EAS AF: 0.139

Gnomad4 SAS AF: 0.176

Gnomad4 FIN AF: 0.404

Gnomad4 NFE AF: 0.302

Gnomad4 OTH AF: 0.235

Alfa AF: 0.257 Hom.: 2565

Bravo AF: 0.235

Asia WGS AF: 0.155 AC: 541 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	5.6
DANN	Benign	0.72

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: rs2268492; hg19: chr3-8800672;