rs3848516

Variant names:

• chr18-57488148-A-G
• rs3848516
• NM_004852.3:c.*11425A>G

Your query was ambiguous. Multiple possible variants found:

• chr18-57488148-A-G
• chr18-57488148-A-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_004852.3(ONECUT2):​c.*11425A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.522 in 152,530 control chromosomes in the GnomAD database, including 24,003 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 (23910 hom., cov: 33)
  • Exomes 𝑓: 0.66 (93 hom.)
• Consequence: ONECUT2 NM_004852.3 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.54
• Publications: 4 publications found

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]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.52).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.683 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_004852.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ONECUT2	NM_004852.3	MANE Select	c.*11425A>G		3_prime_UTR	Exon 2 of 2	NP_004843.2	O95948

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ONECUT2	ENST00000491143.3	TSL:1 MANE Select	c.*11425A>G		3_prime_UTR	Exon 2 of 2	ENSP00000419185.2	O95948

Frequencies

GnomAD3 genomes AF: 0.522 AC: 79383 AN: 151990 Hom.: 23921 Cov.: 33

Gnomad AFR AF: 0.211

Gnomad AMI AF: 0.663

Gnomad AMR AF: 0.494

Gnomad ASJ AF: 0.708

Gnomad EAS AF: 0.517

Gnomad SAS AF: 0.593

Gnomad FIN AF: 0.608

Gnomad MID AF: 0.623

Gnomad NFE AF: 0.688

Gnomad OTH AF: 0.536

GnomAD4 exome AF: 0.659 AC: 278 AN: 422 Hom.: 93 Cov.: 0 AF XY: 0.621 AC XY: 159 AN XY: 256

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.659 AC: 274 AN: 416

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 1.00 AC: 2 AN: 2

Other (OTH) AF: 0.500 AC: 2 AN: 4

GnomAD4 genome AF: 0.522 AC: 79364 AN: 152108 Hom.: 23910 Cov.: 33 AF XY: 0.517 AC XY: 38413 AN XY: 74352

African (AFR) AF: 0.210 AC: 8729 AN: 41498

American (AMR) AF: 0.493 AC: 7532 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.708 AC: 2456 AN: 3470

East Asian (EAS) AF: 0.516 AC: 2669 AN: 5172

South Asian (SAS) AF: 0.591 AC: 2852 AN: 4822

European-Finnish (FIN) AF: 0.608 AC: 6422 AN: 10566

Middle Eastern (MID) AF: 0.609 AC: 179 AN: 294

European-Non Finnish (NFE) AF: 0.688 AC: 46784 AN: 67984

Other (OTH) AF: 0.537 AC: 1136 AN: 2114

Alfa AF: 0.608 Hom.: 17275

Bravo AF: 0.496

Asia WGS AF: 0.553 AC: 1921 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.52
CADD	Benign	6.8
DANN	Benign	0.59
PhyloP100		2.5
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs3848516; hg19: chr18-55155380;