rs16960758

chr15-48314955-T-C

Variant summary

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

The ENST00000560323.1(DUT-AS1):n.303A>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.193 in 152,302 control chromosomes in the GnomAD database, including 3,066 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 0.19 (3065 hom., cov: 33)
  • Exomes 𝑓: 0.19 (1 hom.)
• Consequence: DUT-AS1 ENST00000560323.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.01

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=-0.81).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.264 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC107984755	XR_007064624.1	n.325A>G		non_coding_transcript_exon_variant	1/3
LOC107984755	XR_007064623.1	n.553A>G		non_coding_transcript_exon_variant	2/3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
DUT-AS1	ENST00000560323.1	n.303A>G		non_coding_transcript_exon_variant	2/3	3

Frequencies

GnomAD3 genomes AF: 0.193 AC: 29343 AN: 152146 Hom.: 3060 Cov.: 33

Gnomad AFR AF: 0.268

Gnomad AMI AF: 0.0515

Gnomad AMR AF: 0.196

Gnomad ASJ AF: 0.191

Gnomad EAS AF: 0.190

Gnomad SAS AF: 0.214

Gnomad FIN AF: 0.132

Gnomad MID AF: 0.196

Gnomad NFE AF: 0.156

Gnomad OTH AF: 0.209

GnomAD4 exome AF: 0.194 AC: 7 AN: 36 Hom.: 1 Cov.: 0 AF XY: 0.250 AC XY: 6 AN XY: 24

Gnomad4 AFR exome AF: 0.500

Gnomad4 NFE exome AF: 0.133

Gnomad4 OTH exome AF: 0.500

GnomAD4 genome AF: 0.193 AC: 29382 AN: 152266 Hom.: 3065 Cov.: 33 AF XY: 0.190 AC XY: 14187 AN XY: 74478

Gnomad4 AFR AF: 0.268

Gnomad4 AMR AF: 0.196

Gnomad4 ASJ AF: 0.191

Gnomad4 EAS AF: 0.190

Gnomad4 SAS AF: 0.212

Gnomad4 FIN AF: 0.132

Gnomad4 NFE AF: 0.156

Gnomad4 OTH AF: 0.214

Alfa AF: 0.174 Hom.: 615

Bravo AF: 0.201

Asia WGS AF: 0.227 AC: 787 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
Cadd	Benign	6.0
Dann	Benign	0.80

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs16960758; hg19: chr15-48607152;