rs1994356

Variant names:

• chr12-54177381-T-C
• rs1994356
• ENST00000509864.5:n.396+5123A>G

Variant summary

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

The ENST00000509864.5(SMUG1):​n.396+5123A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.717 in 152,130 control chromosomes in the GnomAD database, including 39,658 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 0.72 (39658 hom., cov: 32)
• Consequence: SMUG1 ENST00000509864.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.621
• Publications: 1 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=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.836 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000509864.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

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

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SMUG1	ENST00000509864.5	TSL:3	n.396+5123A>G		intron	N/A	ENSP00000426440.1	H0YA95
	SMUG1	ENST00000635234.1	TSL:5	n.116-5272A>G		intron	N/A
	SMUG1	ENST00000635546.1	TSL:5	n.406-2234A>G		intron	N/A	ENSP00000489489.1	A0A0U1RRE6

Frequencies

GnomAD3 genomes AF: 0.717 AC: 108992 AN: 152012 Hom.: 39642 Cov.: 32

Gnomad AFR AF: 0.844

Gnomad AMI AF: 0.593

Gnomad AMR AF: 0.624

Gnomad ASJ AF: 0.685

Gnomad EAS AF: 0.633

Gnomad SAS AF: 0.816

Gnomad FIN AF: 0.708

Gnomad MID AF: 0.707

Gnomad NFE AF: 0.665

Gnomad OTH AF: 0.714

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

GnomAD4 genome AF: 0.717 AC: 109049 AN: 152130 Hom.: 39658 Cov.: 32 AF XY: 0.718 AC XY: 53406 AN XY: 74358

African (AFR) AF: 0.844 AC: 35029 AN: 41522

American (AMR) AF: 0.623 AC: 9517 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.685 AC: 2374 AN: 3468

East Asian (EAS) AF: 0.633 AC: 3275 AN: 5172

South Asian (SAS) AF: 0.816 AC: 3936 AN: 4822

European-Finnish (FIN) AF: 0.708 AC: 7495 AN: 10586

Middle Eastern (MID) AF: 0.692 AC: 202 AN: 292

European-Non Finnish (NFE) AF: 0.665 AC: 45182 AN: 67970

Other (OTH) AF: 0.710 AC: 1499 AN: 2110

Alfa AF: 0.690 Hom.: 4748

Bravo AF: 0.711

Asia WGS AF: 0.725 AC: 2524 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	11
DANN	Benign	0.72
PhyloP100		0.62

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs1994356;

hg19: chr12-54571165;