rs2279400

chr12-54187530-G-Achr12-54187530-G-C

Variant summary

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

The NM_001243787.2(SMUG1):c.-20+289C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.482 in 152,024 control chromosomes in the GnomAD database, including 18,336 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 0.48 (18336 hom., cov: 32)
• Consequence: SMUG1 NM_001243787.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.342

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=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.54 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SMUG1	NM_001243787.2	c.-20+289C>T		intron_variant		ENST00000682136.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SMUG1	ENST00000682136.1	c.-20+289C>T		intron_variant			NM_001243787.2	P1

Frequencies

GnomAD3 genomes AF: 0.483 AC: 73329 AN: 151906 Hom.: 18337 Cov.: 32

Gnomad AFR AF: 0.361

Gnomad AMI AF: 0.428

Gnomad AMR AF: 0.480

Gnomad ASJ AF: 0.494

Gnomad EAS AF: 0.385

Gnomad SAS AF: 0.478

Gnomad FIN AF: 0.612

Gnomad MID AF: 0.491

Gnomad NFE AF: 0.544

Gnomad OTH AF: 0.500

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

GnomAD4 genome AF: 0.482 AC: 73350 AN: 152024 Hom.: 18336 Cov.: 32 AF XY: 0.485 AC XY: 36037 AN XY: 74302

Gnomad4 AFR AF: 0.361

Gnomad4 AMR AF: 0.480

Gnomad4 ASJ AF: 0.494

Gnomad4 EAS AF: 0.384

Gnomad4 SAS AF: 0.477

Gnomad4 FIN AF: 0.612

Gnomad4 NFE AF: 0.544

Gnomad4 OTH AF: 0.496

Alfa AF: 0.504 Hom.: 9583

Bravo AF: 0.465

Asia WGS AF: 0.423 AC: 1476 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	1.6
Dann	Benign	0.38

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: rs2279400; hg19: chr12-54581314;