18-49650541-A-G

Position:

• chr18-49650541-A-G

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

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

LOC112268210 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC112268210	XR_002958207.2	n.28A>G		non_coding_transcript_exon_variant	1/2
LOC105372112	XR_007066363.1	n.179-11493A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SMUG1P1	ENST00000590640.1	n.192A>G		non_coding_transcript_exon_variant	1/1

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

Gnomad4 AFR exome AF: 0.669

Gnomad4 AMR exome AF: 0.492

Gnomad4 ASJ exome AF: 0.425

Gnomad4 EAS exome AF: 0.619

Gnomad4 SAS exome AF: 0.422

Gnomad4 FIN exome AF: 0.394

Gnomad4 NFE exome AF: 0.406

Gnomad4 OTH exome AF: 0.433

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

Gnomad4 AFR AF: 0.667

Gnomad4 AMR AF: 0.448

Gnomad4 ASJ AF: 0.455

Gnomad4 EAS AF: 0.550

Gnomad4 SAS AF: 0.436

Gnomad4 FIN AF: 0.374

Gnomad4 NFE AF: 0.413

Gnomad4 OTH AF: 0.484

Alfa AF: 0.421 Hom.: 9773

Bravo AF: 0.506

Asia WGS AF: 0.542 AC: 1885 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4939887; hg19: chr18-47176911;