Variant rs629737 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_004852.3(ONECUT2):c.*6316A>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.388 in 151,898 control chromosomes in the GnomAD database, including 11,901 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 ( 11873 hom., cov: 30)

Exomes 𝑓: 0.34 ( 28 hom. )

Consequence

ONECUT2
NM_004852.3 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.711

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 -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.59).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.469 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.*6316A>C		3_prime_UTR_variant	2/2	ENST00000491143.3	NP_004843.2
ONECUT2	XM_047437947.1 linkuse as main transcript	c.*6527A>C		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.*6316A>C		3_prime_UTR_variant	2/2	1	NM_004852.3	ENSP00000419185	P1

Frequencies

GnomAD3 genomes

AF:

0.387

AC:

58629

AN:

151354

Hom.:

11832

Cov.:

show subpopulations

Gnomad AFR

AF:

0.474

Gnomad AMI

AF:

0.335

Gnomad AMR

AF:

0.467

Gnomad ASJ

AF:

0.291

Gnomad EAS

AF:

0.482

Gnomad SAS

AF:

0.406

Gnomad FIN

AF:

0.390

Gnomad MID

AF:

0.354

Gnomad NFE

AF:

0.314

Gnomad OTH

AF:

0.391

GnomAD4 exome

AF:

0.345

AC:

149

AN:

432

Hom.:

Cov.:

AF XY:

0.373

AC XY:

AN XY:

260

show subpopulations

Gnomad4 FIN exome

AF:

0.345

Gnomad4 NFE exome

AF:

0.00

Gnomad4 OTH exome

AF:

0.500

GnomAD4 genome

AF:

0.388

AC:

58734

AN:

151466

Hom.:

11873

Cov.:

AF XY:

0.396

AC XY:

29321

AN XY:

74014

show subpopulations

Gnomad4 AFR

AF:

0.474

Gnomad4 AMR

AF:

0.468

Gnomad4 ASJ

AF:

0.291

Gnomad4 EAS

AF:

0.483

Gnomad4 SAS

AF:

0.408

Gnomad4 FIN

AF:

0.390

Gnomad4 NFE

AF:

0.314

Gnomad4 OTH

AF:

0.391

Alfa

AF:

0.359

Hom.:

2901

Bravo

AF:

0.399

Asia WGS

AF:

0.428

AC:

1487

AN:

3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.59

CADD

Benign

8.7

DANN

Benign

0.73

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