rs8037626

chr15-48314149-A-G

Variant summary

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

The ENST00000560323.1(DUT-AS1):n.363+746T>C variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.176 in 149,982 control chromosomes in the GnomAD database, including 2,432 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 0.18 (2432 hom., cov: 29)
• Consequence: DUT-AS1 ENST00000560323.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.332

Genes affected

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

LOC107984755 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.214 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC107984755	XR_007064624.1	n.386-673T>C		intron_variant, non_coding_transcript_variant
LOC107984755	XR_007064623.1	n.614-673T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
DUT-AS1	ENST00000560323.1	n.363+746T>C		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.176 AC: 26317 AN: 149880 Hom.: 2424 Cov.: 29

Gnomad AFR AF: 0.217

Gnomad AMI AF: 0.0520

Gnomad AMR AF: 0.192

Gnomad ASJ AF: 0.191

Gnomad EAS AF: 0.119

Gnomad SAS AF: 0.181

Gnomad FIN AF: 0.137

Gnomad MID AF: 0.201

Gnomad NFE AF: 0.157

Gnomad OTH AF: 0.198

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

GnomAD4 genome AF: 0.176 AC: 26360 AN: 149982 Hom.: 2432 Cov.: 29 AF XY: 0.173 AC XY: 12638 AN XY: 73088

Gnomad4 AFR AF: 0.218

Gnomad4 AMR AF: 0.192

Gnomad4 ASJ AF: 0.191

Gnomad4 EAS AF: 0.119

Gnomad4 SAS AF: 0.181

Gnomad4 FIN AF: 0.137

Gnomad4 NFE AF: 0.157

Gnomad4 OTH AF: 0.203

Alfa AF: 0.171 Hom.: 366

Bravo AF: 0.180

Asia WGS AF: 0.184 AC: 639 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
Cadd	Benign	4.9
Dann	Benign	0.85

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs8037626; hg19: chr15-48606346;