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

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.242

Links

OXTR (HGNC:8529):

CAV3 (HGNC:1529):

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
OXTR	NM_000916.4 linkuse as main transcript	c.922+6724C>T		intron_variant		ENST00000316793.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
OXTR	ENST00000316793.8 linkuse as main transcript	c.922+6724C>T		intron_variant		1	NM_000916.4	P1
CAV3	ENST00000472766.1 linkuse as main transcript	n.156-16935G>A		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes

AF:

0.161

AC:

24436

AN:

152088

Hom.:

2310

Cov.:

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Links

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over