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GeneBe

rs2254298

Variant summary

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

The NM_000916(OXTR):c.922+6724C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.161 in 152088 control chromosomes in the gnomAD Genomes database, including 2310 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 0.16 ( 2310 hom., cov: 33)

Consequence

OXTR
NM_000916 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.242

Links

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.86).
BA1
?
GnomAd highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.3 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
OXTRNM_000916.4 linkuse as main transcriptc.922+6724C>T intron_variant ENST00000316793.8

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
OXTRENST00000316793.8 linkuse as main transcriptc.922+6724C>T intron_variant 1 NM_000916.4 P1
CAV3ENST00000472766.1 linkuse as main transcriptn.156-16935G>A intron_variant, non_coding_transcript_variant 2

Frequencies

GnomAD3 genomes
AF:
0.161
AC:
24436
AN:
152088
Hom.:
2310
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.226
Gnomad AMI
AF:
0.136
Gnomad AMR
AF:
0.210
Gnomad ASJ
AF:
0.206
Gnomad EAS
AF:
0.313
Gnomad SAS
AF:
0.109
Gnomad FIN
AF:
0.0735
Gnomad MID
AF:
0.231
Gnomad NFE
AF:
0.113
Gnomad OTH
AF:
0.178
Alfa
AF:
0.140
Hom.:
559
Bravo
AF:
0.177
Asia WGS
AF:
0.245
AC:
850
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.86
Cadd
Benign
4.1
Dann
Benign
0.35

Splicing

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: rs2254298; hg19: chr3-8802228;