rs34097556

Positions:

• chr20-3072305-C-CA
• chr20-3072305-C-CAA

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1

The ENST00000217386.2(OXT):​c.322+28dup variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.168 in 1,599,508 control chromosomes in the GnomAD database, including 23,271 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.16 (2089 hom., cov: 30)
  • Exomes 𝑓: 0.17 (21182 hom.)
• Consequence: OXT ENST00000217386.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.11

Genes affected

OXT (HGNC:8528): (oxytocin/neurophysin I prepropeptide) This gene encodes a precursor protein that is processed to produce oxytocin and neurophysin I. Oxytocin is a posterior pituitary hormone which is synthesized as an inactive precursor in the hypothalamus along with its carrier protein neurophysin I. Together with neurophysin, it is packaged into neurosecretory vesicles and transported axonally to the nerve endings in the neurohypophysis, where it is either stored or secreted into the bloodstream. The precursor seems to be activated while it is being transported along the axon to the posterior pituitary. This hormone contracts smooth muscle during parturition and lactation. It is also involved in cognition, tolerance, adaptation and complex sexual and maternal behaviour, as well as in the regulation of water excretion and cardiovascular functions. [provided by RefSeq, Dec 2013]

LOC101929098 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -8 ACMG points.

• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.178 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
OXT	NM_000915.4	c.322+28dup		intron_variant		ENST00000217386.2	NP_000906.1
LOC101929098	XR_430278.4			upstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
OXT	ENST00000217386.2	c.322+28dup		intron_variant		1	NM_000915.4	ENSP00000217386	P1

Frequencies

GnomAD3 genomes AF: 0.162 AC: 24599 AN: 152042 Hom.: 2082 Cov.: 30

Gnomad AFR AF: 0.164

Gnomad AMI AF: 0.195

Gnomad AMR AF: 0.119

Gnomad ASJ AF: 0.206

Gnomad EAS AF: 0.0740

Gnomad SAS AF: 0.187

Gnomad FIN AF: 0.177

Gnomad MID AF: 0.207

Gnomad NFE AF: 0.170

Gnomad OTH AF: 0.169

GnomAD3 exomes AF: 0.154 AC: 35029 AN: 227194 Hom.: 2981 AF XY: 0.161 AC XY: 20267 AN XY: 126206

Gnomad AFR exome AF: 0.163

Gnomad AMR exome AF: 0.0806

Gnomad ASJ exome AF: 0.206

Gnomad EAS exome AF: 0.0721

Gnomad SAS exome AF: 0.195

Gnomad FIN exome AF: 0.172

Gnomad NFE exome AF: 0.172

Gnomad OTH exome AF: 0.164

GnomAD4 exome AF: 0.169 AC: 244454 AN: 1447352 Hom.: 21182 Cov.: 33 AF XY: 0.170 AC XY: 122720 AN XY: 720364

Gnomad4 AFR exome AF: 0.168

Gnomad4 AMR exome AF: 0.0841

Gnomad4 ASJ exome AF: 0.200

Gnomad4 EAS exome AF: 0.0724

Gnomad4 SAS exome AF: 0.196

Gnomad4 FIN exome AF: 0.174

Gnomad4 NFE exome AF: 0.173

Gnomad4 OTH exome AF: 0.167

GnomAD4 genome AF: 0.162 AC: 24616 AN: 152156 Hom.: 2089 Cov.: 30 AF XY: 0.162 AC XY: 12016 AN XY: 74402

Gnomad4 AFR AF: 0.164

Gnomad4 AMR AF: 0.118

Gnomad4 ASJ AF: 0.206

Gnomad4 EAS AF: 0.0738

Gnomad4 SAS AF: 0.188

Gnomad4 FIN AF: 0.177

Gnomad4 NFE AF: 0.170

Gnomad4 OTH AF: 0.168

Alfa AF: 0.167 Hom.: 361

Asia WGS AF: 0.126 AC: 437 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Other links and lift over

dbSNP: rs34097556; hg19: chr20-3052951;