18-49650541-A-G

Variant names:

• chr18-49650541-A-G
• rs4939887
• ENST00000590640.1:n.192A>G

Variant summary

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

The ENST00000590640.1(SMUG1P1):​n.192A>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.471 in 213,604 control chromosomes in the GnomAD database, including 25,163 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 0.49 (19176 hom., cov: 31)
  • Exomes 𝑓: 0.42 (5987 hom.)
• Consequence: SMUG1P1 ENST00000590640.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.39
• Publications: 7 publications found

Genes affected

SMUG1P1 (HGNC:49401): (single-strand-selective monofunctional uracil-DNA glycosylase 1 pseudogene 1)

ENSG00000310339 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.67).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.66 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000590640.1. 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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SMUG1P1	ENST00000590640.1	TSL:6	n.192A>G		non_coding_transcript_exon	Exon 1 of 1
	ENSG00000310339	ENST00000849189.1		n.30A>G		non_coding_transcript_exon	Exon 1 of 4
	ENSG00000310339	ENST00000849193.1		n.57A>G		non_coding_transcript_exon	Exon 1 of 2

Frequencies

GnomAD3 genomes AF: 0.490 AC: 74174 AN: 151400 Hom.: 19134 Cov.: 31

Gnomad AFR AF: 0.667

Gnomad AMI AF: 0.373

Gnomad AMR AF: 0.447

Gnomad ASJ AF: 0.455

Gnomad EAS AF: 0.550

Gnomad SAS AF: 0.436

Gnomad FIN AF: 0.374

Gnomad MID AF: 0.449

Gnomad NFE AF: 0.413

Gnomad OTH AF: 0.479

GnomAD4 exome AF: 0.423 AC: 26265 AN: 62086 Hom.: 5987 Cov.: 0 AF XY: 0.426 AC XY: 14312 AN XY: 33576

African (AFR) AF: 0.669 AC: 644 AN: 962

American (AMR) AF: 0.492 AC: 1290 AN: 2622

Ashkenazi Jewish (ASJ) AF: 0.425 AC: 434 AN: 1020

East Asian (EAS) AF: 0.619 AC: 982 AN: 1586

South Asian (SAS) AF: 0.422 AC: 3539 AN: 8378

European-Finnish (FIN) AF: 0.394 AC: 4607 AN: 11700

Middle Eastern (MID) AF: 0.491 AC: 874 AN: 1780

European-Non Finnish (NFE) AF: 0.406 AC: 12527 AN: 30882

Other (OTH) AF: 0.433 AC: 1368 AN: 3156

GnomAD4 genome AF: 0.490 AC: 74280 AN: 151518 Hom.: 19176 Cov.: 31 AF XY: 0.485 AC XY: 35899 AN XY: 74034

African (AFR) AF: 0.667 AC: 27535 AN: 41282

American (AMR) AF: 0.448 AC: 6825 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.455 AC: 1575 AN: 3460

East Asian (EAS) AF: 0.550 AC: 2804 AN: 5098

South Asian (SAS) AF: 0.436 AC: 2101 AN: 4820

European-Finnish (FIN) AF: 0.374 AC: 3931 AN: 10512

Middle Eastern (MID) AF: 0.459 AC: 135 AN: 294

European-Non Finnish (NFE) AF: 0.413 AC: 28025 AN: 67810

Other (OTH) AF: 0.484 AC: 1013 AN: 2094

Alfa AF: 0.430 Hom.: 14200

Bravo AF: 0.506

Asia WGS AF: 0.542 AC: 1885 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.67
CADD	Benign	0.44
DANN	Benign	0.32
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs4939887; hg19: chr18-47176911;