rs11170826

Variant names:

• chr12-54138168-T-C
• rs11170826
• ENST00000634429.1:n.688-8416A>G

Variant summary

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

The ENST00000634429.1(SMUG1):​n.688-8416A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.128 in 152,288 control chromosomes in the GnomAD database, including 1,421 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 0.13 (1421 hom., cov: 33)
• Consequence: SMUG1 ENST00000634429.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.57
• Publications: 2 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]

LINC02381 (HGNC:53304): (long intergenic non-protein coding RNA 2381)

FAM242C (HGNC:53873): (family with sequence similarity 242 member C)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.201 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000634429.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SMUG1	ENST00000634429.1	TSL:5	n.688-8416A>G		intron	N/A
	LINC02381	ENST00000635070.1	TSL:5	n.401-2078T>C		intron	N/A
	SMUG1	ENST00000635234.1	TSL:5	n.306-16713A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.128 AC: 19415 AN: 152170 Hom.: 1417 Cov.: 33

Gnomad AFR AF: 0.204

Gnomad AMI AF: 0.0636

Gnomad AMR AF: 0.0999

Gnomad ASJ AF: 0.0937

Gnomad EAS AF: 0.00250

Gnomad SAS AF: 0.186

Gnomad FIN AF: 0.0842

Gnomad MID AF: 0.111

Gnomad NFE AF: 0.102

Gnomad OTH AF: 0.127

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

GnomAD4 genome AF: 0.128 AC: 19435 AN: 152288 Hom.: 1421 Cov.: 33 AF XY: 0.126 AC XY: 9373 AN XY: 74468

African (AFR) AF: 0.204 AC: 8487 AN: 41532

American (AMR) AF: 0.0996 AC: 1523 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.0937 AC: 325 AN: 3468

East Asian (EAS) AF: 0.00250 AC: 13 AN: 5196

South Asian (SAS) AF: 0.186 AC: 900 AN: 4828

European-Finnish (FIN) AF: 0.0842 AC: 894 AN: 10618

Middle Eastern (MID) AF: 0.109 AC: 32 AN: 294

European-Non Finnish (NFE) AF: 0.102 AC: 6939 AN: 68032

Other (OTH) AF: 0.125 AC: 264 AN: 2116

Alfa AF: 0.111 Hom.: 183

Bravo AF: 0.129

Asia WGS AF: 0.103 AC: 360 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.11
DANN	Benign	0.30
PhyloP100		-2.6

Splicing

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

Other links and lift over

dbSNP: rs11170826; hg19: chr12-54531952;