dbSNP rs11170826: SMUG1:n.688-8416A>G (chr12-54138168-T-C) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000635546.1(SMUG1):n.*289-16713A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.128 in 152,288 control chromosomes in the GnomAD database, including 1,421 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 0.13 ( 1421 hom., cov: 33)

Consequence

SMUG1
ENST00000635546.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.57

Variant links:

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]

SMUG1 links:

LINC02381 (HGNC:53304): (long intergenic non-protein coding RNA 2381)

LINC02381 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.9).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.201 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
SMUG1	ENST00000634429.1 link	n.688-8416A>G	intron_variant	Intron 4 of 5	5
LINC02381	ENST00000635070.1 link	n.401-2078T>C	intron_variant	Intron 1 of 2	5
SMUG1	ENST00000635234.1 link	n.306-16713A>G	intron_variant	Intron 4 of 4	5

Frequencies

GnomAD3 genomes

AF:

0.128

AC:

19415

AN:

152170

Hom.:

1417

Cov.:

show subpopulations

Gnomad AFR

AF:

0.204

Gnomad AMI

AF:

0.0636

Gnomad AMR

AF:

0.0999

Gnomad ASJ

AF:

0.0937

Gnomad EAS

AF:

0.00250

Gnomad SAS

AF:

0.186

Gnomad FIN

AF:

0.0842

Gnomad MID

AF:

0.111

Gnomad NFE

AF:

0.102

Gnomad OTH

AF:

0.127

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

GnomAD4 genome

AF:

0.128

AC:

19435

AN:

152288

Hom.:

1421

Cov.:

AF XY:

0.126

AC XY:

9373

AN XY:

74468

show subpopulations

Gnomad4 AFR

AF:

0.204

Gnomad4 AMR

AF:

0.0996

Gnomad4 ASJ

AF:

0.0937

Gnomad4 EAS

AF:

0.00250

Gnomad4 SAS

AF:

0.186

Gnomad4 FIN

AF:

0.0842

Gnomad4 NFE

AF:

0.102

Gnomad4 OTH

AF:

0.125

Alfa

AF:

0.109

Hom.:

176

Bravo

AF:

0.129

Asia WGS

AF:

0.103

AC:

360

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

0.11

DANN

Benign

0.30

Splicing

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over