rs2279400

Variant names:

• chr12-54187530-G-A
• rs2279400
• NM_001243787.2:c.-20+289C>T

Your query was ambiguous. Multiple possible variants found:

• chr12-54187530-G-A
• chr12-54187530-G-C

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 12 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=-0.9).
• 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 rank	MANE	Protein	UniProt
SMUG1	NM_001243787.2	c.-20+289C>T		intron_variant	Intron 2 of 3	ENST00000682136.1	NP_001230716.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SMUG1	ENST00000682136.1	c.-20+289C>T		intron_variant	Intron 2 of 3		NM_001243787.2	ENSP00000507590.1

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

African (AFR) AF: 0.361 AC: 14977 AN: 41450

American (AMR) AF: 0.480 AC: 7335 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.494 AC: 1715 AN: 3472

East Asian (EAS) AF: 0.384 AC: 1985 AN: 5164

South Asian (SAS) AF: 0.477 AC: 2299 AN: 4816

European-Finnish (FIN) AF: 0.612 AC: 6470 AN: 10568

Middle Eastern (MID) AF: 0.476 AC: 140 AN: 294

European-Non Finnish (NFE) AF: 0.544 AC: 36994 AN: 67972

Other (OTH) AF: 0.496 AC: 1047 AN: 2112

Alfa AF: 0.500 Hom.: 13741

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
PhyloP100		-0.34
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs2279400; hg19: chr12-54581314;