15-48315886-G-A

Variant names:

• chr15-48315886-G-A
• rs11631385
• ENST00000560323.1:n.295-923C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000560323.1(DUT-AS1):​n.295-923C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.617 in 152,060 control chromosomes in the GnomAD database, including 34,269 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 (34269 hom., cov: 32)
• Consequence: DUT-AS1 ENST00000560323.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.887
• Publications: 5 publications found

Genes affected

DUT-AS1 (HGNC:55420): (DUT antisense RNA 1)

ENSG00000303148 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.816 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000560323.1. 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
	DUT-AS1	NR_186809.1		n.295-923C>T		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DUT-AS1	ENST00000560323.1	TSL:3	n.295-923C>T		intron	N/A
	ENSG00000303148	ENST00000792186.1		n.189+2206G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.617 AC: 93763 AN: 151942 Hom.: 34280 Cov.: 32

Gnomad AFR AF: 0.223

Gnomad AMI AF: 0.899

Gnomad AMR AF: 0.683

Gnomad ASJ AF: 0.785

Gnomad EAS AF: 0.361

Gnomad SAS AF: 0.597

Gnomad FIN AF: 0.792

Gnomad MID AF: 0.769

Gnomad NFE AF: 0.821

Gnomad OTH AF: 0.652

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

GnomAD4 genome AF: 0.617 AC: 93754 AN: 152060 Hom.: 34269 Cov.: 32 AF XY: 0.617 AC XY: 45831 AN XY: 74340

African (AFR) AF: 0.222 AC: 9222 AN: 41452

American (AMR) AF: 0.682 AC: 10411 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.785 AC: 2725 AN: 3470

East Asian (EAS) AF: 0.361 AC: 1862 AN: 5160

South Asian (SAS) AF: 0.600 AC: 2892 AN: 4818

European-Finnish (FIN) AF: 0.792 AC: 8390 AN: 10590

Middle Eastern (MID) AF: 0.759 AC: 223 AN: 294

European-Non Finnish (NFE) AF: 0.821 AC: 55844 AN: 67986

Other (OTH) AF: 0.646 AC: 1365 AN: 2112

Alfa AF: 0.572 Hom.: 2401

Bravo AF: 0.592

Asia WGS AF: 0.443 AC: 1544 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.14
DANN	Benign	0.41
PhyloP100		-0.89

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: rs11631385;

hg19: chr15-48608083;