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3-8753043-C-T

Variant summary

Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2

The NM_000916.4(OXTR):c.1104G>A(p.Ser368=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00214 in 1,614,136 control chromosomes in the GnomAD database, including 9 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.0017 ( 0 hom., cov: 32)
Exomes 𝑓: 0.0022 ( 9 hom. )

Consequence

OXTR
NM_000916.4 synonymous

Scores

2

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -3.46
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 -11 ACMG points.

BP4
?
    BP4 - Multiple lines of computational evidence suggest no impact on gene or gene product (conservation, evolutionary, splicing impact, etc.)
Computational evidence support a benign effect (BayesDel_noAF=-0.66).
BP6
?
    BP6 - Reputable source recently reports variant as benign, but the evidence is not available to the laboratory to perform an independent evaluation
Variant 3-8753043-C-T is Benign according to our data. Variant chr3-8753043-C-T is described in ClinVar as [Benign]. Clinvar id is 723037.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
    BP7 - A synonymous (silent) variant for which splicing prediction algorithms predict no impact to the splice consensus sequence nor the creation of a new splice site AND the nucleotide is not highly conserved
Synonymous conserved (PhyloP=-3.46 with no splicing effect.
BS2
?
    BS2 - Observed in a healthy adult individual for a recessive (homozygous), dominant (heterozygous), or X-linked (hemizygous) disorder, with full penetrance expected at an early age
High AC in GnomAd at 259 AD gene.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
OXTRNM_000916.4 linkuse as main transcriptc.1104G>A p.Ser368= synonymous_variant 4/4 ENST00000316793.8

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
OXTRENST00000316793.8 linkuse as main transcriptc.1104G>A p.Ser368= synonymous_variant 4/41 NM_000916.4 P1
CAV3ENST00000472766.1 linkuse as main transcriptn.155+19053C>T intron_variant, non_coding_transcript_variant 2

Frequencies

GnomAD3 genomes
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.00170
AC:
259
AN:
152180
Hom.:
0
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.000386
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00183
Gnomad ASJ
AF:
0.00403
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00124
Gnomad FIN
AF:
0.0000942
Gnomad MID
AF:
0.00633
Gnomad NFE
AF:
0.00270
Gnomad OTH
AF:
0.00382
GnomAD3 exomes
AF:
0.00200
AC:
501
AN:
251002
Hom.:
1
AF XY:
0.00216
AC XY:
293
AN XY:
135678
show subpopulations
Gnomad AFR exome
AF:
0.000493
Gnomad AMR exome
AF:
0.00168
Gnomad ASJ exome
AF:
0.00646
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.000751
Gnomad FIN exome
AF:
0.000185
Gnomad NFE exome
AF:
0.00288
Gnomad OTH exome
AF:
0.00278
GnomAD4 exome
AF:
0.00218
AC:
3193
AN:
1461838
Hom.:
9
Cov.:
32
AF XY:
0.00217
AC XY:
1581
AN XY:
727226
show subpopulations
Gnomad4 AFR exome
AF:
0.000388
Gnomad4 AMR exome
AF:
0.00188
Gnomad4 ASJ exome
AF:
0.00509
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.000962
Gnomad4 FIN exome
AF:
0.000206
Gnomad4 NFE exome
AF:
0.00235
Gnomad4 OTH exome
AF:
0.00343
GnomAD4 genome
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.00170
AC:
259
AN:
152298
Hom.:
0
Cov.:
32
AF XY:
0.00141
AC XY:
105
AN XY:
74464
show subpopulations
Gnomad4 AFR
AF:
0.000385
Gnomad4 AMR
AF:
0.00183
Gnomad4 ASJ
AF:
0.00403
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00124
Gnomad4 FIN
AF:
0.0000942
Gnomad4 NFE
AF:
0.00271
Gnomad4 OTH
AF:
0.00378
Alfa
AF:
0.00265
Hom.:
0
Bravo
AF:
0.00193
Asia WGS
AF:
0.00115
AC:
4
AN:
3478
EpiCase
AF:
0.00382
EpiControl
AF:
0.00379

ClinVar

Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not provided Benign:1
Benign, criteria provided, single submitterclinical testingInvitaeJul 10, 2018- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.66
Cadd
Benign
1.4
Dann
Benign
0.77

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: rs148736817; hg19: chr3-8794729; API