rs10161263

Variant names:

• chr12-54179559-T-C
• rs10161263
• ENST00000509864.5:n.396+2945A>G

Variant summary

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

The ENST00000509864.5(SMUG1):​n.396+2945A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.718 in 151,994 control chromosomes in the GnomAD database, including 39,694 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 0.72 (39694 hom., cov: 31)
• Consequence: SMUG1 ENST00000509864.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.180
• Publications: 15 publications found

Genes affected

SMUG1 (HGNC:17148): (single-strand-selective monofunctional uracil-DNA glycosylase 1) This gene encodes a protein that participates in base excision repair by removing uracil from single- and double-stranded DNA. Many alternatively spliced transcript variants exist for this gene; the full-length nature is known for some but not all of the variants. [provided by RefSeq, Aug 2011]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.836 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000509864.5. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SMUG1	ENST00000509864.5	TSL:3	n.396+2945A>G		intron	N/A	ENSP00000426440.1	H0YA95
	SMUG1	ENST00000635234.1	TSL:5	n.116-7450A>G		intron	N/A
	SMUG1	ENST00000635546.1	TSL:5	n.405+2945A>G		intron	N/A	ENSP00000489489.1	A0A0U1RRE6

Frequencies

GnomAD3 genomes AF: 0.718 AC: 109005 AN: 151876 Hom.: 39676 Cov.: 31

Gnomad AFR AF: 0.844

Gnomad AMI AF: 0.595

Gnomad AMR AF: 0.626

Gnomad ASJ AF: 0.688

Gnomad EAS AF: 0.636

Gnomad SAS AF: 0.800

Gnomad FIN AF: 0.707

Gnomad MID AF: 0.734

Gnomad NFE AF: 0.667

Gnomad OTH AF: 0.716

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.718 AC: 109065 AN: 151994 Hom.: 39694 Cov.: 31 AF XY: 0.719 AC XY: 53423 AN XY: 74308

African (AFR) AF: 0.844 AC: 34961 AN: 41444

American (AMR) AF: 0.625 AC: 9541 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.688 AC: 2387 AN: 3470

East Asian (EAS) AF: 0.636 AC: 3281 AN: 5158

South Asian (SAS) AF: 0.800 AC: 3854 AN: 4816

European-Finnish (FIN) AF: 0.707 AC: 7482 AN: 10578

Middle Eastern (MID) AF: 0.721 AC: 212 AN: 294

European-Non Finnish (NFE) AF: 0.667 AC: 45304 AN: 67942

Other (OTH) AF: 0.712 AC: 1502 AN: 2110

Alfa AF: 0.682 Hom.: 110338

Bravo AF: 0.712

Asia WGS AF: 0.720 AC: 2506 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.7
DANN	Benign	0.30
PhyloP100		-0.18

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs10161263; hg19: chr12-54573343;