rs3136392

Variant names:

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

Your query was ambiguous. Multiple possible variants found:

• chr12-54181762-C-A
• chr12-54181762-C-T

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_001243787.2(SMUG1):​c.*334G>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000769 in 1,300,124 control chromosomes in the GnomAD database, with no homozygous occurrence. 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: not found (cov: 33)
  • Exomes 𝑓: 7.7e-7 (0 hom.)
• Consequence: SMUG1 NM_001243787.2 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.470
• Publications: 0 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: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001243787.2. 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
	SMUG1	NM_001243787.2	MANE Select	c.*334G>T		3_prime_UTR	Exon 4 of 4	NP_001230716.1
	SMUG1	NM_001243788.2		c.*334G>T		3_prime_UTR	Exon 3 of 3	NP_001230717.1
	SMUG1	NM_001351242.2		c.*334G>T		3_prime_UTR	Exon 4 of 4	NP_001338171.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SMUG1	ENST00000682136.1	MANE Select	c.*334G>T		3_prime_UTR	Exon 4 of 4	ENSP00000507590.1
	SMUG1	ENST00000243112.9	TSL:1	c.406-115G>T		intron	N/A	ENSP00000243112.5
	SMUG1	ENST00000513838.5	TSL:1	c.406-115G>T		intron	N/A	ENSP00000423629.1

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome AF: 7.69e-7 AC: 1 AN: 1300124 Hom.: 0 Cov.: 34 AF XY: 0.00000158 AC XY: 1 AN XY: 632630

⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.

African (AFR) AF: 0.00 AC: 0 AN: 28932

American (AMR) AF: 0.00 AC: 0 AN: 23396

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 20010

East Asian (EAS) AF: 0.00 AC: 0 AN: 35058

South Asian (SAS) AF: 0.00 AC: 0 AN: 63788

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 30926

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 4790

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 1038920

Other (OTH) AF: 0.0000184 AC: 1 AN: 54304

⚠️ The allele balance in gnomAD4 Exomes is highly skewed from 0.5 (p-value = 0), which strongly suggests a high chance of mosaicism in these individuals.

GnomAD4 genome Cov.: 33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	2.8
DANN	Benign	0.57
PhyloP100		-0.47

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: rs3136392; hg19: chr12-54575546;