Variant rs608823 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_ModerateBA1

The NM_004852.3(ONECUT2):c.*11915G>A variant causes a 3 prime UTR change. The variant allele was found at a frequency of 0.385 in 152,566 control chromosomes in the GnomAD database, including 11,858 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 0.39 ( 11830 hom., cov: 33)

Exomes 𝑓: 0.35 ( 28 hom. )

Consequence

ONECUT2
NM_004852.3 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 5.89

Variant links:

Genes affected

ONECUT2 (HGNC:8139): (one cut homeobox 2) This gene encodes a member of the onecut family of transcription factors, which are characterized by a cut domain and an atypical homeodomain. The protein binds to specific DNA sequences and stimulates expression of target genes, including genes involved in melanocyte and hepatocyte differentiation. [provided by RefSeq, Jul 2008]

ONECUT2 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.31).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.468 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ONECUT2	NM_004852.3 linkuse as main transcript	c.*11915G>A		3_prime_UTR_variant	2/2	ENST00000491143.3	NP_004843.2
ONECUT2	XM_047437947.1 linkuse as main transcript	c.*12126G>A		3_prime_UTR_variant	3/3		XP_047293903.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ONECUT2	ENST00000491143.3 linkuse as main transcript	c.*11915G>A		3_prime_UTR_variant	2/2	1	NM_004852.3	ENSP00000419185	P1

Frequencies

GnomAD3 genomes

AF:

0.385

AC:

58551

AN:

152014

Hom.:

11792

Cov.:

show subpopulations

Gnomad AFR

AF:

0.473

Gnomad AMI

AF:

0.336

Gnomad AMR

AF:

0.463

Gnomad ASJ

AF:

0.291

Gnomad EAS

AF:

0.482

Gnomad SAS

AF:

0.404

Gnomad FIN

AF:

0.392

Gnomad MID

AF:

0.351

Gnomad NFE

AF:

0.310

Gnomad OTH

AF:

0.387

GnomAD4 exome

AF:

0.346

AC:

150

AN:

434

Hom.:

Cov.:

AF XY:

0.374

AC XY:

AN XY:

262

show subpopulations

Gnomad4 FIN exome

AF:

0.345

Gnomad4 NFE exome

AF:

0.250

Gnomad4 OTH exome

AF:

0.500

GnomAD4 genome

AF:

0.386

AC:

58649

AN:

152132

Hom.:

11830

Cov.:

AF XY:

0.395

AC XY:

29346

AN XY:

74364

show subpopulations

Gnomad4 AFR

AF:

0.473

Gnomad4 AMR

AF:

0.464

Gnomad4 ASJ

AF:

0.291

Gnomad4 EAS

AF:

0.483

Gnomad4 SAS

AF:

0.406

Gnomad4 FIN

AF:

0.392

Gnomad4 NFE

AF:

0.310

Gnomad4 OTH

AF:

0.386

Alfa

AF:

0.327

Hom.:

13926

Bravo

AF:

0.396

Asia WGS

AF:

0.428

AC:

1488

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.31

CADD

Benign

DANN

Benign

0.87

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over