dbSNP rs3745064: ONECUT2:c.*10111A>G (chr18-57486834-A-G) – ACMG Classification: Benign (-10 pts)

Variant summary

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

The NM_004852.3(ONECUT2):c.*10111A>G variant causes a 3 prime UTR change. The variant allele was found at a frequency of 0.52 in 152,518 control chromosomes in the GnomAD database, including 23,795 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 0.52 ( 23699 hom., cov: 32)

Exomes 𝑓: 0.66 ( 96 hom. )

Consequence

ONECUT2
NM_004852.3 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 3.74

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=-0.42).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.679 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ONECUT2	NM_004852.3 link	c.*10111A>G		3_prime_UTR_variant	Exon 2 of 2	ENST00000491143.3	NP_004843.2	O95948
ONECUT2	XM_047437947.1 link	c.*10322A>G		3_prime_UTR_variant	Exon 3 of 3		XP_047293903.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ONECUT2	ENST00000491143.3 link	c.*10111A>G		3_prime_UTR_variant	Exon 2 of 2	1	NM_004852.3	ENSP00000419185.2		O95948

Frequencies

GnomAD3 genomes

AF:

0.520

AC:

79047

AN:

151966

Hom.:

23709

Cov.:

show subpopulations

Gnomad AFR

AF:

0.210

Gnomad AMI

AF:

0.665

Gnomad AMR

AF:

0.492

Gnomad ASJ

AF:

0.707

Gnomad EAS

AF:

0.518

Gnomad SAS

AF:

0.594

Gnomad FIN

AF:

0.608

Gnomad MID

AF:

0.617

Gnomad NFE

AF:

0.684

Gnomad OTH

AF:

0.533

GnomAD4 exome

AF:

0.657

AC:

285

AN:

434

Hom.:

Cov.:

AF XY:

0.630

AC XY:

165

AN XY:

262

show subpopulations

Gnomad4 FIN exome

AF:

0.657

Gnomad4 NFE exome

AF:

1.00

Gnomad4 OTH exome

AF:

0.500

GnomAD4 genome

AF:

0.520

AC:

79029

AN:

152084

Hom.:

23699

Cov.:

AF XY:

0.515

AC XY:

38283

AN XY:

74334

show subpopulations

Gnomad4 AFR

AF:

0.210

Gnomad4 AMR

AF:

0.491

Gnomad4 ASJ

AF:

0.707

Gnomad4 EAS

AF:

0.517

Gnomad4 SAS

AF:

0.592

Gnomad4 FIN

AF:

0.608

Gnomad4 NFE

AF:

0.684

Gnomad4 OTH

AF:

0.535

Alfa

AF:

0.645

Hom.:

31624

Bravo

AF:

0.494

Asia WGS

AF:

0.552

AC:

1918

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.42

CADD

Benign

DANN

Benign

0.86

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