3-8755399-C-T

Position:

• chr3-8755399-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.923-2175G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.183 in 152,222 control chromosomes in the GnomAD database, including 3,019 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 0.18 (3019 hom., cov: 34)
• Consequence: OXTR NM_000916.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.305

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:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.478 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
OXTR	NM_000916.4	c.923-2175G>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.923-2175G>A		intron_variant		1	NM_000916.4	ENSP00000324270.2
CAV3	ENST00000472766.1	n.155+21409C>T		intron_variant		2

Frequencies

GnomAD3 genomes AF: 0.183 AC: 27863 AN: 152104 Hom.: 3021 Cov.: 34

Gnomad AFR AF: 0.225

Gnomad AMI AF: 0.146

Gnomad AMR AF: 0.244

Gnomad ASJ AF: 0.194

Gnomad EAS AF: 0.493

Gnomad SAS AF: 0.157

Gnomad FIN AF: 0.107

Gnomad MID AF: 0.253

Gnomad NFE AF: 0.133

Gnomad OTH AF: 0.204

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

GnomAD4 genome AF: 0.183 AC: 27891 AN: 152222 Hom.: 3019 Cov.: 34 AF XY: 0.185 AC XY: 13781 AN XY: 74434

Gnomad4 AFR AF: 0.225

Gnomad4 AMR AF: 0.244

Gnomad4 ASJ AF: 0.194

Gnomad4 EAS AF: 0.494

Gnomad4 SAS AF: 0.157

Gnomad4 FIN AF: 0.107

Gnomad4 NFE AF: 0.133

Gnomad4 OTH AF: 0.203

Alfa AF: 0.154 Hom.: 2702

Bravo AF: 0.199

Asia WGS AF: 0.358 AC: 1243 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.99
DANN	Benign	0.27

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: rs2268490; hg19: chr3-8797085;