rs16960758

Variant names:

• chr15-48314955-T-C
• rs16960758
• ENST00000560323.1:n.303A>G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 11 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=-0.81).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.264 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.303A>G		non_coding_transcript_exon	Exon 2 of 3

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DUT-AS1	ENST00000560323.1	TSL:3	n.303A>G		non_coding_transcript_exon	Exon 2 of 3
	ENSG00000303148	ENST00000792186.1		n.189+1275T>C		intron	N/A

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

African (AFR) AF: 0.500 AC: 2 AN: 4

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.133 AC: 4 AN: 30

Other (OTH) AF: 0.500 AC: 1 AN: 2

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

African (AFR) AF: 0.268 AC: 11142 AN: 41534

American (AMR) AF: 0.196 AC: 3004 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.191 AC: 663 AN: 3472

East Asian (EAS) AF: 0.190 AC: 984 AN: 5184

South Asian (SAS) AF: 0.212 AC: 1025 AN: 4832

European-Finnish (FIN) AF: 0.132 AC: 1406 AN: 10612

Middle Eastern (MID) AF: 0.204 AC: 60 AN: 294

European-Non Finnish (NFE) AF: 0.156 AC: 10600 AN: 68018

Other (OTH) AF: 0.214 AC: 451 AN: 2112

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	6.0
DANN	Benign	0.80
PhyloP100		1.0

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: rs16960758;

hg19: chr15-48607152;