Variant 3-8752859-G-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_000916.4(OXTR):c.*118C>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.389 in 1,124,216 control chromosomes in the GnomAD database, including 89,518 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 0.45 ( 16610 hom., cov: 31)

Exomes 𝑓: 0.38 ( 72908 hom. )

Consequence

OXTR
NM_000916.4 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.14

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 -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.92).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.631 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.*118C>A		3_prime_UTR_variant	4/4	ENST00000316793.8	NP_000907.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
OXTR	ENST00000316793.8 linkuse as main transcript	c.*118C>A		3_prime_UTR_variant	4/4	1	NM_000916.4	ENSP00000324270	P1
CAV3	ENST00000472766.1 linkuse as main transcript	n.155+18869G>T		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes

AF:

0.449

AC:

68111

AN:

151594

Hom.:

16568

Cov.:

show subpopulations

Gnomad AFR

AF:

0.637

Gnomad AMI

AF:

0.450

Gnomad AMR

AF:

0.437

Gnomad ASJ

AF:

0.351

Gnomad EAS

AF:

0.0866

Gnomad SAS

AF:

0.353

Gnomad FIN

AF:

0.373

Gnomad MID

AF:

0.354

Gnomad NFE

AF:

0.391

Gnomad OTH

AF:

0.432

GnomAD4 exome

AF:

0.379

AC:

368547

AN:

972504

Hom.:

72908

Cov.:

AF XY:

0.379

AC XY:

182571

AN XY:

481984

show subpopulations

Gnomad4 AFR exome

AF:

0.642

Gnomad4 AMR exome

AF:

0.447

Gnomad4 ASJ exome

AF:

0.355

Gnomad4 EAS exome

AF:

0.0960

Gnomad4 SAS exome

AF:

0.366

Gnomad4 FIN exome

AF:

0.376

Gnomad4 NFE exome

AF:

0.384

Gnomad4 OTH exome

AF:

0.379

GnomAD4 genome

AF:

0.450

AC:

68211

AN:

151712

Hom.:

16610

Cov.:

AF XY:

0.443

AC XY:

32855

AN XY:

74140

show subpopulations

Gnomad4 AFR

AF:

0.637

Gnomad4 AMR

AF:

0.437

Gnomad4 ASJ

AF:

0.351

Gnomad4 EAS

AF:

0.0866

Gnomad4 SAS

AF:

0.353

Gnomad4 FIN

AF:

0.373

Gnomad4 NFE

AF:

0.391

Gnomad4 OTH

AF:

0.430

Alfa

AF:

0.386

Hom.:

14630

Bravo

AF:

0.464

Asia WGS

AF:

0.255

AC:

892

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.92

CADD

Benign

0.054

DANN

Benign

0.61

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