rs2381387

Variant names:

• chr4-39530308-G-A
• rs2381387
• ENST00000504032.1:n.321-1661G>A

Your query was ambiguous. Multiple possible variants found:

• chr4-39530308-G-A
• chr4-39530308-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000504032.1(UGDH-AS1):​n.321-1661G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.615 in 152,034 control chromosomes in the GnomAD database, including 29,042 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 0.62 (29042 hom., cov: 33)
• Consequence: UGDH-AS1 ENST00000504032.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.855

Genes affected

UGDH-AS1 (HGNC:40601): (UGDH antisense RNA 1)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.73 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
UGDH-AS1	NR_047679.1	n.501-1661G>A		intron_variant	Intron 1 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
UGDH-AS1	ENST00000504032.1	n.321-1661G>A		intron_variant	Intron 1 of 4	2
UGDH-AS1	ENST00000685788.2	n.620-1661G>A		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.615 AC: 93475 AN: 151914 Hom.: 29032 Cov.: 33

Gnomad AFR AF: 0.542

Gnomad AMI AF: 0.683

Gnomad AMR AF: 0.680

Gnomad ASJ AF: 0.604

Gnomad EAS AF: 0.750

Gnomad SAS AF: 0.616

Gnomad FIN AF: 0.692

Gnomad MID AF: 0.576

Gnomad NFE AF: 0.624

Gnomad OTH AF: 0.578

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

GnomAD4 genome AF: 0.615 AC: 93523 AN: 152034 Hom.: 29042 Cov.: 33 AF XY: 0.623 AC XY: 46277 AN XY: 74340

Gnomad4 AFR AF: 0.542

Gnomad4 AMR AF: 0.680

Gnomad4 ASJ AF: 0.604

Gnomad4 EAS AF: 0.749

Gnomad4 SAS AF: 0.615

Gnomad4 FIN AF: 0.692

Gnomad4 NFE AF: 0.624

Gnomad4 OTH AF: 0.574

Alfa AF: 0.620 Hom.: 60219

Bravo AF: 0.610

Asia WGS AF: 0.623 AC: 2167 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.81
DANN	Benign	0.58

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2381387; hg19: chr4-39531928;