Variant rs674849 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.*2931C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.335 in 152,482 control chromosomes in the GnomAD database, including 9,064 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 0.33 ( 9048 hom., cov: 32)

Exomes 𝑓: 0.28 ( 16 hom. )

Consequence

ONECUT2
NM_004852.3 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 3.53

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=-0.45).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.447 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.*2931C>T		3_prime_UTR_variant	2/2	ENST00000491143.3	NP_004843.2
ONECUT2	XM_047437947.1 linkuse as main transcript	c.*3142C>T		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.*2931C>T		3_prime_UTR_variant	2/2	1	NM_004852.3	ENSP00000419185	P1

Frequencies

GnomAD3 genomes

AF:

0.335

AC:

50854

AN:

151918

Hom.:

9027

Cov.:

show subpopulations

Gnomad AFR

AF:

0.452

Gnomad AMI

AF:

0.332

Gnomad AMR

AF:

0.292

Gnomad ASJ

AF:

0.285

Gnomad EAS

AF:

0.112

Gnomad SAS

AF:

0.386

Gnomad FIN

AF:

0.324

Gnomad MID

AF:

0.329

Gnomad NFE

AF:

0.290

Gnomad OTH

AF:

0.337

GnomAD4 exome

AF:

0.283

AC:

127

AN:

448

Hom.:

Cov.:

AF XY:

0.293

AC XY:

AN XY:

270

show subpopulations

Gnomad4 AFR exome

AF:

0.500

Gnomad4 FIN exome

AF:

0.279

Gnomad4 NFE exome

AF:

0.375

Gnomad4 OTH exome

AF:

0.250

GnomAD4 genome

AF:

0.335

AC:

50926

AN:

152034

Hom.:

9048

Cov.:

AF XY:

0.337

AC XY:

25075

AN XY:

74302

show subpopulations

Gnomad4 AFR

AF:

0.453

Gnomad4 AMR

AF:

0.292

Gnomad4 ASJ

AF:

0.285

Gnomad4 EAS

AF:

0.112

Gnomad4 SAS

AF:

0.388

Gnomad4 FIN

AF:

0.324

Gnomad4 NFE

AF:

0.290

Gnomad4 OTH

AF:

0.338

Alfa

AF:

0.302

Hom.:

3551

Bravo

AF:

0.332

Asia WGS

AF:

0.274

AC:

954

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.45

CADD

Benign

DANN

Benign

0.79

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