rs34097556

Variant names:

• chr20-3072305-C-CA
• rs34097556
• NM_000915.4:c.322+28dupA

Your query was ambiguous. Multiple possible variants found:

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

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BA1

The NM_000915.4(OXT):​c.322+28dupA 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 NM_000915.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.11
• Publications: 7 publications found

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]

ENSG00000305741 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -8 ACMG points.

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

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_000915.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	OXT	NM_000915.4	MANE Select	c.322+28dupA		intron	N/A	NP_000906.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	OXT	ENST00000217386.2	TSL:1 MANE Select	c.322+27_322+28insA		intron	N/A	ENSP00000217386.2
	ENSG00000305741	ENST00000812739.1		n.-22_-21insT		upstream_gene	N/A

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

GnomAD2 exomes AF: 0.154 AC: 35029 AN: 227194 AF XY: 0.161

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 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

African (AFR) AF: 0.168 AC: 5611 AN: 33422

American (AMR) AF: 0.0841 AC: 3753 AN: 44606

Ashkenazi Jewish (ASJ) AF: 0.200 AC: 5211 AN: 26012

East Asian (EAS) AF: 0.0724 AC: 2871 AN: 39646

South Asian (SAS) AF: 0.196 AC: 16877 AN: 86070

European-Finnish (FIN) AF: 0.174 AC: 7202 AN: 41440

Middle Eastern (MID) AF: 0.158 AC: 898 AN: 5674

European-Non Finnish (NFE) AF: 0.173 AC: 191990 AN: 1110384

Other (OTH) AF: 0.167 AC: 10041 AN: 60098

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

African (AFR) AF: 0.164 AC: 6791 AN: 41532

American (AMR) AF: 0.118 AC: 1810 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.206 AC: 716 AN: 3470

East Asian (EAS) AF: 0.0738 AC: 381 AN: 5160

South Asian (SAS) AF: 0.188 AC: 909 AN: 4828

European-Finnish (FIN) AF: 0.177 AC: 1876 AN: 10584

Middle Eastern (MID) AF: 0.212 AC: 62 AN: 292

European-Non Finnish (NFE) AF: 0.170 AC: 11539 AN: 67972

Other (OTH) AF: 0.168 AC: 355 AN: 2112

Alfa AF: 0.167 Hom.: 361

Asia WGS AF: 0.126 AC: 437 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		-1.1
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs34097556; hg19: chr20-3052951; COSMIC: COSV105095394;