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. The variant received -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
• Publications: 20 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000504032.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	UGDH-AS1	NR_047679.1		n.501-1661G>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	UGDH-AS1	ENST00000504032.1	TSL:2	n.321-1661G>A		intron	N/A
	UGDH-AS1	ENST00000685788.3		n.627-1661G>A		intron	N/A
	UGDH-AS1	ENST00000718929.1		n.336+1970G>A		intron	N/A

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

African (AFR) AF: 0.542 AC: 22449 AN: 41440

American (AMR) AF: 0.680 AC: 10402 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.604 AC: 2096 AN: 3468

East Asian (EAS) AF: 0.749 AC: 3874 AN: 5170

South Asian (SAS) AF: 0.615 AC: 2970 AN: 4828

European-Finnish (FIN) AF: 0.692 AC: 7292 AN: 10538

Middle Eastern (MID) AF: 0.572 AC: 167 AN: 292

European-Non Finnish (NFE) AF: 0.624 AC: 42438 AN: 67982

Other (OTH) AF: 0.574 AC: 1212 AN: 2112

Alfa AF: 0.620 Hom.: 126690

Bravo AF: 0.610

Asia WGS AF: 0.623 AC: 2167 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.81
DANN	Benign	0.58
PhyloP100		-0.85

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs2381387;

hg19: chr4-39531928;