Variant rs2228485 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_ModerateBA1

The ENST00000316793.8(OXTR):c.171C>T(p.Asn57=) variant causes a synonymous change. The variant allele was found at a frequency of 0.748 in 1,605,674 control chromosomes in the GnomAD database, including 450,697 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 0.71 ( 39182 hom., cov: 33)

Exomes 𝑓: 0.75 ( 411515 hom. )

Consequence

OXTR
ENST00000316793.8 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 4.98

Variant links:

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]

OXTR links:

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]

CAV3 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.43).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.814 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
OXTR	NM_000916.4 linkuse as main transcript	c.171C>T	p.Asn57=	synonymous_variant	3/4	ENST00000316793.8	NP_000907.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris
OXTR	ENST00000316793.8 linkuse as main transcript	c.171C>T	p.Asn57=	synonymous_variant	3/4	1	NM_000916.4	ENSP00000324270	P1
OXTR	ENST00000449615.1 linkuse as main transcript	c.171C>T	p.Asn57=	synonymous_variant	2/2	2		ENSP00000389587
CAV3	ENST00000472766.1 linkuse as main transcript	n.156-9460G>A		intron_variant, non_coding_transcript_variant		2
OXTR	ENST00000431493.1 linkuse as main transcript			downstream_gene_variant		4		ENSP00000414828

Frequencies

GnomAD3 genomes

AF:

0.715

AC:

108647

AN:

152002

Hom.:

39177

Cov.:

show subpopulations

Gnomad AFR

AF:

0.640

Gnomad AMI

AF:

0.783

Gnomad AMR

AF:

0.648

Gnomad ASJ

AF:

0.739

Gnomad EAS

AF:

0.715

Gnomad SAS

AF:

0.836

Gnomad FIN

AF:

0.787

Gnomad MID

AF:

0.748

Gnomad NFE

AF:

0.753

Gnomad OTH

AF:

0.715

GnomAD3 exomes

AF:

0.734

AC:

170474

AN:

232408

Hom.:

63102

AF XY:

0.746

AC XY:

94682

AN XY:

126864

show subpopulations

Gnomad AFR exome

AF:

0.637

Gnomad AMR exome

AF:

0.591

Gnomad ASJ exome

AF:

0.753

Gnomad EAS exome

AF:

0.725

Gnomad SAS exome

AF:

0.827

Gnomad FIN exome

AF:

0.784

Gnomad NFE exome

AF:

0.756

Gnomad OTH exome

AF:

0.735

GnomAD4 exome

AF:

0.751

AC:

1091879

AN:

1453556

Hom.:

411515

Cov.:

AF XY:

0.754

AC XY:

544803

AN XY:

722500

show subpopulations

Gnomad4 AFR exome

AF:

0.633

Gnomad4 AMR exome

AF:

0.598

Gnomad4 ASJ exome

AF:

0.749

Gnomad4 EAS exome

AF:

0.684

Gnomad4 SAS exome

AF:

0.823

Gnomad4 FIN exome

AF:

0.777

Gnomad4 NFE exome

AF:

0.757

Gnomad4 OTH exome

AF:

0.744

GnomAD4 genome

AF:

0.715

AC:

108697

AN:

152118

Hom.:

39182

Cov.:

AF XY:

0.718

AC XY:

53415

AN XY:

74352

show subpopulations

Gnomad4 AFR

AF:

0.640

Gnomad4 AMR

AF:

0.648

Gnomad4 ASJ

AF:

0.739

Gnomad4 EAS

AF:

0.715

Gnomad4 SAS

AF:

0.835

Gnomad4 FIN

AF:

0.787

Gnomad4 NFE

AF:

0.753

Gnomad4 OTH

AF:

0.710

Alfa

AF:

0.740

Hom.:

17266

Bravo

AF:

0.699

Asia WGS

AF:

0.734

AC:

2555

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.43

CADD

Benign

7.2

DANN

Benign

0.96

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over