dbSNP rs34115976: UGT8:c.823-7154C>A (chr4-114656841-C-A) – ACMG Classification: Likely_benign (-2 pts)

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2BP4_Strong

The NM_001128174.3(UGT8):c.823-7154C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 32)

Exomes 𝑓: 0.0 ( 0 hom. )

Failed GnomAD Quality Control

Consequence

UGT8
NM_001128174.3 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.711

Publications

18 publications found

Variant links:

Genes affected

UGT8 (HGNC:12555): (UDP glycosyltransferase 8) The protein encoded by this gene belongs to the UDP-glycosyltransferase family. It catalyzes the transfer of galactose to ceramide, a key enzymatic step in the biosynthesis of galactocerebrosides, which are abundant sphingolipids of the myelin membrane of the central and peripheral nervous systems. Alternatively spliced transcript variants have been found for this gene. [provided by RefSeq, Sep 2011]

UGT8 links:

MIR577 (HGNC:32833): (microRNA 577) microRNAs (miRNAs) are short (20-24 nt) non-coding RNAs that are involved in post-transcriptional regulation of gene expression in multicellular organisms by affecting both the stability and translation of mRNAs. miRNAs are transcribed by RNA polymerase II as part of capped and polyadenylated primary transcripts (pri-miRNAs) that can be either protein-coding or non-coding. The primary transcript is cleaved by the Drosha ribonuclease III enzyme to produce an approximately 70-nt stem-loop precursor miRNA (pre-miRNA), which is further cleaved by the cytoplasmic Dicer ribonuclease to generate the mature miRNA and antisense miRNA star (miRNA*) products. The mature miRNA is incorporated into a RNA-induced silencing complex (RISC), which recognizes target mRNAs through imperfect base pairing with the miRNA and most commonly results in translational inhibition or destabilization of the target mRNA. The RefSeq represents the predicted microRNA stem-loop. [provided by RefSeq, Sep 2009]

MIR577 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Likely_benign. The variant received -2 ACMG points.

PM2

Very rare variant in population databases, with high coverage;

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.88).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
UGT8	NM_001128174.3 link	c.823-7154C>A		intron_variant	Intron 2 of 5	ENST00000310836.11	NP_001121646.2

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein
UGT8	ENST00000310836.11 link	c.823-7154C>A	intron_variant	Intron 2 of 5	1	NM_001128174.3	ENSP00000311648.6
UGT8	ENST00000394511.3 link	c.823-7154C>A	intron_variant	Intron 1 of 4	1		ENSP00000378019.3
MIR577	ENST00000385196.1 link	n.83C>A	non_coding_transcript_exon_variant	Exon 1 of 1	6
UGT8	ENST00000507710.2 link	c.823-7154C>A	intron_variant	Intron 3 of 6	3		ENSP00000421446.2

Frequencies

GnomAD3 genomes

Cov.:

GnomAD4 exome

Data not reliable, filtered out with message: AC0

AF:

0.00

AC:

AN:

359294

Hom.:

Cov.:

AF XY:

0.00

AC XY:

AN XY:

204080

African (AFR)

AF:

0.00

AC:

AN:

10036

American (AMR)

AF:

0.00

AC:

AN:

34446

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

11118

East Asian (EAS)

AF:

0.00

AC:

AN:

12846

South Asian (SAS)

AF:

0.00

AC:

AN:

63422

European-Finnish (FIN)

AF:

0.00

AC:

AN:

30972

Middle Eastern (MID)

AF:

0.00

AC:

AN:

2620

European-Non Finnish (NFE)

AF:

0.00

AC:

AN:

178196

Other (OTH)

AF:

0.00

AC:

AN:

15638

GnomAD4 genome

Cov.:

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.88

CADD

Benign

0.33

(source)

DANN

Benign

0.58

PhyloP100

-0.71

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

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

Other links and lift over