Genetic Variant OXT:c.*191C>A (chr20-3072609-C-A) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_000915.4(OXT):c.*191C>A variant causes a downstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.308 in 662,150 control chromosomes in the GnomAD database, including 33,015 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 0.28 ( 6541 hom., cov: 32)

Exomes 𝑓: 0.32 ( 26474 hom. )

Consequence

OXT
NM_000915.4 downstream_gene

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.243

Publications

46 publications found

Variant links:

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]

OXT links:

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.89).

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.38 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
OXT	NM_000915.4 link	c.*191C>A		downstream_gene_variant		ENST00000217386.2	NP_000906.1	P01178X5D7M6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
OXT	ENST00000217386.2 link	c.*191C>A		downstream_gene_variant		1	NM_000915.4	ENSP00000217386.2		P01178

Frequencies

GnomAD3 genomes

AF:

0.282

AC:

42854

AN:

151836

Hom.:

6527

Cov.:

show subpopulations

Gnomad AFR

AF:

0.175

Gnomad AMI

AF:

0.158

Gnomad AMR

AF:

0.387

Gnomad ASJ

AF:

0.301

Gnomad EAS

AF:

0.283

Gnomad SAS

AF:

0.272

Gnomad FIN

AF:

0.271

Gnomad MID

AF:

0.259

Gnomad NFE

AF:

0.328

Gnomad OTH

AF:

0.262

GnomAD4 exome

AF:

0.316

AC:

161033

AN:

510196

Hom.:

26474

AF XY:

0.312

AC XY:

83561

AN XY:

267966

show subpopulations

African (AFR)

AF:

0.174

AC:

2363

AN:

13552

American (AMR)

AF:

0.472

AC:

12060

AN:

25540

Ashkenazi Jewish (ASJ)

AF:

0.298

AC:

4519

AN:

15172

East Asian (EAS)

AF:

0.276

AC:

8520

AN:

30814

South Asian (SAS)

AF:

0.260

AC:

13008

AN:

50052

European-Finnish (FIN)

AF:

0.288

AC:

8672

AN:

30162

Middle Eastern (MID)

AF:

0.266

AC:

679

AN:

2552

European-Non Finnish (NFE)

AF:

0.326

AC:

102351

AN:

314192

Other (OTH)

AF:

0.315

AC:

8861

AN:

28160

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

5609

11217

16826

22434

28043

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

1032

2064

3096

4128

5160

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.282

AC:

42893

AN:

151954

Hom.:

6541

Cov.:

AF XY:

0.282

AC XY:

20938

AN XY:

74246

show subpopulations

African (AFR)

AF:

0.175

AC:

7251

AN:

41470

American (AMR)

AF:

0.388

AC:

5926

AN:

15264

Ashkenazi Jewish (ASJ)

AF:

0.301

AC:

1044

AN:

3468

East Asian (EAS)

AF:

0.283

AC:

1453

AN:

5130

South Asian (SAS)

AF:

0.272

AC:

1312

AN:

4816

European-Finnish (FIN)

AF:

0.271

AC:

2865

AN:

10572

Middle Eastern (MID)

AF:

0.262

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.328

AC:

22267

AN:

67924

Other (OTH)

AF:

0.263

AC:

554

AN:

2104

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.495

Heterozygous variant carriers

1490

2980

4471

5961

7451

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

450

900

1350

1800

2250

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.301

Hom.:

8197

Bravo

AF:

0.288

Asia WGS

AF:

0.326

AC:

1135

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.89

CADD

Benign

2.7

(source)

DANN

Benign

0.84

PhyloP100

-0.24

Mutation Taster

=92/8

polymorphism

(source)

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over