12-54181762-C-T

Variant names:

• chr12-54181762-C-T
• rs3136392
• NM_001243787.2:c.*334G>A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001243787.2(SMUG1):​c.*334G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0065 in 1,452,408 control chromosomes in the GnomAD database, including 539 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 0.033 (294 hom., cov: 33)
  • Exomes 𝑓: 0.0034 (245 hom.)
• Consequence: SMUG1 NM_001243787.2 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.470

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=-0.83).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.111 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SMUG1	NM_001243787.2	c.*334G>A		3_prime_UTR_variant	Exon 4 of 4	ENST00000682136.1	NP_001230716.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SMUG1	ENST00000682136	c.*334G>A		3_prime_UTR_variant	Exon 4 of 4		NM_001243787.2	ENSP00000507590.1

Frequencies

GnomAD3 genomes AF: 0.0329 AC: 5004 AN: 152174 Hom.: 293 Cov.: 33

Gnomad AFR AF: 0.114

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0128

Gnomad ASJ AF: 0.000864

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.000414

Gnomad FIN AF: 0.000377

Gnomad MID AF: 0.00949

Gnomad NFE AF: 0.000514

Gnomad OTH AF: 0.0272

GnomAD4 exome AF: 0.00340 AC: 4414 AN: 1300116 Hom.: 245 Cov.: 34 AF XY: 0.00299 AC XY: 1894 AN XY: 632628

Gnomad4 AFR exome AF: 0.118

Gnomad4 AMR exome AF: 0.00876

Gnomad4 ASJ exome AF: 0.00160

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.000423

Gnomad4 FIN exome AF: 0.000194

Gnomad4 NFE exome AF: 0.000224

Gnomad4 OTH exome AF: 0.00834

GnomAD4 genome AF: 0.0330 AC: 5023 AN: 152292 Hom.: 294 Cov.: 33 AF XY: 0.0317 AC XY: 2357 AN XY: 74462

Gnomad4 AFR AF: 0.114

Gnomad4 AMR AF: 0.0127

Gnomad4 ASJ AF: 0.000864

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.000207

Gnomad4 FIN AF: 0.000377

Gnomad4 NFE AF: 0.000514

Gnomad4 OTH AF: 0.0270

Alfa AF: 0.0264 Hom.: 33

Bravo AF: 0.0374

Asia WGS AF: 0.00577 AC: 20 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	3.5
DANN	Benign	0.48

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

Other links and lift over

dbSNP: rs3136392; hg19: chr12-54575546;