Variant 9-111932206-A-G details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1

The NM_003358.3(UGCG):c.861A>G(p.Thr287=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.278 in 1,613,606 control chromosomes in the GnomAD database, including 64,130 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 0.31 ( 7576 hom., cov: 32)

Exomes 𝑓: 0.27 ( 56554 hom. )

Consequence

UGCG
NM_003358.3 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.339

Variant links:

Genes affected

UGCG (HGNC:12524): (UDP-glucose ceramide glucosyltransferase) This gene encodes an enzyme that catalyzes the first glycosylation step in the biosynthesis of glycosphingolipids, which are membrane components containing lipid and sugar moieties. The product of this reaction is glucosylceramide, which is the core structure of many glycosphingolipids. [provided by RefSeq, Dec 2014]

UGCG links:

MIR4668 (HGNC:41545): (microRNA 4668) 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]

MIR4668 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -13 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.56).

BP7

Synonymous conserved (PhyloP=0.339 with no splicing effect.

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.392 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE
UGCG	NM_003358.3 linkuse as main transcript	c.861A>G	p.Thr287=	synonymous_variant	8/9	ENST00000374279.4
UGCG	XM_047423844.1 linkuse as main transcript	c.477A>G	p.Thr159=	synonymous_variant	8/9
MIR4668	NR_039814.1 linkuse as main transcript			downstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
UGCG	ENST00000374279.4 linkuse as main transcript	c.861A>G	p.Thr287=	synonymous_variant	8/9	1	NM_003358.3	P1
MIR4668	ENST00000582284.1 linkuse as main transcript			downstream_gene_variant

Frequencies

GnomAD3 genomes

AF:

0.309

AC:

46862

AN:

151858

Hom.:

7565

Cov.:

show subpopulations

Gnomad AFR

AF:

0.356

Gnomad AMI

AF:

0.257

Gnomad AMR

AF:

0.400

Gnomad ASJ

AF:

0.231

Gnomad EAS

AF:

0.274

Gnomad SAS

AF:

0.266

Gnomad FIN

AF:

0.328

Gnomad MID

AF:

0.296

Gnomad NFE

AF:

0.267

Gnomad OTH

AF:

0.287

GnomAD3 exomes

AF:

0.308

AC:

77356

AN:

251300

Hom.:

12689

AF XY:

0.298

AC XY:

40478

AN XY:

135832

show subpopulations

Gnomad AFR exome

AF:

0.358

Gnomad AMR exome

AF:

0.482

Gnomad ASJ exome

AF:

0.220

Gnomad EAS exome

AF:

0.274

Gnomad SAS exome

AF:

0.272

Gnomad FIN exome

AF:

0.315

Gnomad NFE exome

AF:

0.270

Gnomad OTH exome

AF:

0.294

GnomAD4 exome

AF:

0.274

AC:

400919

AN:

1461630

Hom.:

56554

Cov.:

AF XY:

0.273

AC XY:

198477

AN XY:

727146

show subpopulations

Gnomad4 AFR exome

AF:

0.360

Gnomad4 AMR exome

AF:

0.467

Gnomad4 ASJ exome

AF:

0.223

Gnomad4 EAS exome

AF:

0.236

Gnomad4 SAS exome

AF:

0.269

Gnomad4 FIN exome

AF:

0.316

Gnomad4 NFE exome

AF:

0.265

Gnomad4 OTH exome

AF:

0.272

GnomAD4 genome

AF:

0.309

AC:

46926

AN:

151976

Hom.:

7576

Cov.:

AF XY:

0.313

AC XY:

23274

AN XY:

74278

show subpopulations

Gnomad4 AFR

AF:

0.357

Gnomad4 AMR

AF:

0.401

Gnomad4 ASJ

AF:

0.231

Gnomad4 EAS

AF:

0.274

Gnomad4 SAS

AF:

0.267

Gnomad4 FIN

AF:

0.328

Gnomad4 NFE

AF:

0.267

Gnomad4 OTH

AF:

0.286

Alfa

AF:

0.280

Hom.:

8345

Bravo

AF:

0.317

Asia WGS

AF:

0.277

AC:

961

AN:

3478

EpiCase

AF:

0.260

EpiControl

AF:

0.260

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.56

CADD

Benign

8.0

DANN

Benign

0.69

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.7

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