rs10161263

Variant names:

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

Variant summary

Our verdict is Benign. Variant got -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

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

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SMUG1	XR_007063064.1	n.1467+2945A>G		intron_variant	Intron 4 of 6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SMUG1	ENST00000509864.5	n.396+2945A>G		intron_variant	Intron 2 of 4	3		ENSP00000426440.1
SMUG1	ENST00000635234.1	n.116-7450A>G		intron_variant	Intron 2 of 4	5
SMUG1	ENST00000635546.1	n.405+2945A>G		intron_variant	Intron 4 of 8	5		ENSP00000489489.1

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

Gnomad4 AFR AF: 0.844

Gnomad4 AMR AF: 0.625

Gnomad4 ASJ AF: 0.688

Gnomad4 EAS AF: 0.636

Gnomad4 SAS AF: 0.800

Gnomad4 FIN AF: 0.707

Gnomad4 NFE AF: 0.667

Gnomad4 OTH AF: 0.712

Alfa AF: 0.673 Hom.: 69298

Bravo AF: 0.712

Asia WGS AF: 0.720 AC: 2506 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10161263; hg19: chr12-54573343;