chr15-48325151-C-T

Variant names:

• chr15-48325151-C-T
• rs8042136
• ENST00000560323.1:n.294+6412G>A

Variant summary

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

The ENST00000560323.1(DUT-AS1):​n.294+6412G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.965 in 152,276 control chromosomes in the GnomAD database, including 71,053 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 0.96 (71053 hom., cov: 32)
• Consequence: DUT-AS1 ENST00000560323.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.85
• Publications: 2 publications found

Genes affected

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

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.993 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DUT-AS1	NR_186809.1	n.294+6412G>A		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DUT-AS1	ENST00000560323.1	n.294+6412G>A		intron_variant	Intron 1 of 2	3

Frequencies

GnomAD3 genomes AF: 0.965 AC: 146817 AN: 152160 Hom.: 71022 Cov.: 32

Gnomad AFR AF: 0.887

Gnomad AMI AF: 1.00

Gnomad AMR AF: 0.981

Gnomad ASJ AF: 1.00

Gnomad EAS AF: 0.969

Gnomad SAS AF: 0.970

Gnomad FIN AF: 1.00

Gnomad MID AF: 0.997

Gnomad NFE AF: 1.00

Gnomad OTH AF: 0.973

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

GnomAD4 genome AF: 0.965 AC: 146904 AN: 152276 Hom.: 71053 Cov.: 32 AF XY: 0.965 AC XY: 71833 AN XY: 74466

African (AFR) AF: 0.887 AC: 36797 AN: 41496

American (AMR) AF: 0.981 AC: 15012 AN: 15308

Ashkenazi Jewish (ASJ) AF: 1.00 AC: 3472 AN: 3472

East Asian (EAS) AF: 0.969 AC: 5024 AN: 5184

South Asian (SAS) AF: 0.970 AC: 4691 AN: 4834

European-Finnish (FIN) AF: 1.00 AC: 10618 AN: 10618

Middle Eastern (MID) AF: 0.997 AC: 293 AN: 294

European-Non Finnish (NFE) AF: 1.00 AC: 68027 AN: 68044

Other (OTH) AF: 0.974 AC: 2058 AN: 2114

Alfa AF: 0.976 Hom.: 25647

Bravo AF: 0.960

Asia WGS AF: 0.953 AC: 3314 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.81
DANN	Benign	0.49
PhyloP100		-1.9

Splicing

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

Other links and lift over

dbSNP: rs8042136; hg19: chr15-48617348;