rs61740241
Positions:
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The NM_000916.4(OXTR):c.712G>A(p.Ala238Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.027 in 1,604,954 control chromosomes in the GnomAD database, including 697 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.020 ( 36 hom., cov: 33)
Exomes 𝑓: 0.028 ( 661 hom. )
Consequence
OXTR
NM_000916.4 missense
NM_000916.4 missense
Scores
1
17
Clinical Significance
Conservation
PhyloP100: 1.42
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 -14 ACMG points.
BP4
?
Computational evidence support a benign effect (MetaRNN=0.002678454).
BP6
?
Variant 3-8767476-C-T is Benign according to our data. Variant chr3-8767476-C-T is described in ClinVar as [Benign]. Clinvar id is 3037365.Status of the report is criteria_provided_single_submitter, 1 stars.
BS1
?
Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0195 (2976/152322) while in subpopulation NFE AF= 0.0297 (2023/68008). AF 95% confidence interval is 0.0287. There are 36 homozygotes in gnomad4. There are 1397 alleles in male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck.
BS2
?
High AC in GnomAd4 at 2976 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
OXTR | NM_000916.4 | c.712G>A | p.Ala238Thr | missense_variant | 3/4 | ENST00000316793.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
OXTR | ENST00000316793.8 | c.712G>A | p.Ala238Thr | missense_variant | 3/4 | 1 | NM_000916.4 | P1 | |
CAV3 | ENST00000472766.1 | n.156-10001C>T | intron_variant, non_coding_transcript_variant | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.0196 AC: 2977AN: 152212Hom.: 36 Cov.: 33
GnomAD3 genomes
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GnomAD3 exomes AF: 0.0199 AC: 4521AN: 226688Hom.: 67 AF XY: 0.0201 AC XY: 2491AN XY: 124206
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GnomAD4 exome AF: 0.0278 AC: 40344AN: 1452632Hom.: 661 Cov.: 30 AF XY: 0.0270 AC XY: 19507AN XY: 721884
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GnomAD4 genome ? AF: 0.0195 AC: 2976AN: 152322Hom.: 36 Cov.: 33 AF XY: 0.0188 AC XY: 1397AN XY: 74488
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107
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124
ESP6500AA
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34
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225
ExAC
?
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2328
Asia WGS
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3472
ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
OXTR-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Feb 11, 2020 | This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
DEOGEN2
Benign
T
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Benign
D
LIST_S2
Benign
T
MetaRNN
Benign
T
MetaSVM
Benign
T
MutationAssessor
Benign
N
MutationTaster
Benign
N
PrimateAI
Uncertain
T
PROVEAN
Benign
N
REVEL
Benign
Sift
Benign
T
Sift4G
Benign
T
Polyphen
B
Vest4
MPC
ClinPred
T
GERP RS
Varity_R
gMVP
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at