Variant rs2233921 details in Genebe, Genetics Data Aggregator

Variant summary

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

The NM_001243787.2(SMUG1):c.*80G>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 0.449 in 1,510,624 control chromosomes in the GnomAD database, including 158,229 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 0.36 ( 12093 hom., cov: 31)

Exomes 𝑓: 0.46 ( 146136 hom. )

Consequence

SMUG1
NM_001243787.2 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.300

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:

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=-0.87).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.467 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SMUG1	NM_001243787.2 linkuse as main transcript	c.*80G>T		3_prime_UTR_variant	4/4	ENST00000682136.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SMUG1	ENST00000682136.1 linkuse as main transcript	c.*80G>T		3_prime_UTR_variant	4/4		NM_001243787.2	P1	Q53HV7-1

Frequencies

GnomAD3 genomes

AF:

0.362

AC:

54912

AN:

151788

Hom.:

12101

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0991

Gnomad AMI

AF:

0.405

Gnomad AMR

AF:

0.406

Gnomad ASJ

AF:

0.416

Gnomad EAS

AF:

0.394

Gnomad SAS

AF:

0.396

Gnomad FIN

AF:

0.557

Gnomad MID

AF:

0.475

Gnomad NFE

AF:

0.471

Gnomad OTH

AF:

0.396

GnomAD4 exome

AF:

0.459

AC:

623011

AN:

1358718

Hom.:

146136

Cov.:

AF XY:

0.458

AC XY:

304443

AN XY:

664578

show subpopulations

Gnomad4 AFR exome

AF:

0.0832

Gnomad4 AMR exome

AF:

0.383

Gnomad4 ASJ exome

AF:

0.422

Gnomad4 EAS exome

AF:

0.403

Gnomad4 SAS exome

AF:

0.400

Gnomad4 FIN exome

AF:

0.545

Gnomad4 NFE exome

AF:

0.475

Gnomad4 OTH exome

AF:

0.442

GnomAD4 genome

AF:

0.361

AC:

54884

AN:

151906

Hom.:

12093

Cov.:

AF XY:

0.368

AC XY:

27327

AN XY:

74232

show subpopulations

Gnomad4 AFR

AF:

0.0988

Gnomad4 AMR

AF:

0.406

Gnomad4 ASJ

AF:

0.416

Gnomad4 EAS

AF:

0.393

Gnomad4 SAS

AF:

0.395

Gnomad4 FIN

AF:

0.557

Gnomad4 NFE

AF:

0.472

Gnomad4 OTH

AF:

0.393

Alfa

AF:

0.422

Hom.:

6613

Bravo

AF:

0.338

Asia WGS

AF:

0.362

AC:

1261

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.87

CADD

Benign

4.9

DANN

Benign

0.52

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

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