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GeneBe

rs53576

Variant summary

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

The NM_000916.4(OXTR):c.922+4581T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.682 in 152,162 control chromosomes in the GnomAD database, including 36,029 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 0.68 ( 36029 hom., cov: 33)

Consequence

OXTR
NM_000916.4 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.572
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]
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]

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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 = 0.774 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
OXTRNM_000916.4 linkuse as main transcriptc.922+4581T>C intron_variant ENST00000316793.8

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
OXTRENST00000316793.8 linkuse as main transcriptc.922+4581T>C intron_variant 1 NM_000916.4 P1
CAV3ENST00000472766.1 linkuse as main transcriptn.156-14792A>G intron_variant, non_coding_transcript_variant 2

Frequencies

GnomAD3 genomes
AF:
0.682
AC:
103688
AN:
152046
Hom.:
35996
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.781
Gnomad AMI
AF:
0.786
Gnomad AMR
AF:
0.654
Gnomad ASJ
AF:
0.705
Gnomad EAS
AF:
0.348
Gnomad SAS
AF:
0.585
Gnomad FIN
AF:
0.539
Gnomad MID
AF:
0.646
Gnomad NFE
AF:
0.680
Gnomad OTH
AF:
0.677
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.682
AC:
103774
AN:
152162
Hom.:
36029
Cov.:
33
AF XY:
0.671
AC XY:
49914
AN XY:
74382
show subpopulations
Gnomad4 AFR
AF:
0.781
Gnomad4 AMR
AF:
0.654
Gnomad4 ASJ
AF:
0.705
Gnomad4 EAS
AF:
0.348
Gnomad4 SAS
AF:
0.586
Gnomad4 FIN
AF:
0.539
Gnomad4 NFE
AF:
0.680
Gnomad4 OTH
AF:
0.676
Alfa
AF:
0.674
Hom.:
17063
Bravo
AF:
0.693
Asia WGS
AF:
0.499
AC:
1733
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
7.0
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.

Other links and lift over

dbSNP: rs53576; hg19: chr3-8804371; API