rs11631385

Positions:

• chr15-48315886-G-A
• chr15-48315886-G-T

Variant summary

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

The ENST00000560323.1(DUT-AS1):​n.295-923C>T 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 0.617 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, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.887

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=-0.95).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.816 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC107984755	XR_007064623.1	n.545-923C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
DUT-AS1	ENST00000560323.1	n.295-923C>T		intron_variant, non_coding_transcript_variant		3

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

Gnomad4 AFR AF: 0.222

Gnomad4 AMR AF: 0.682

Gnomad4 ASJ AF: 0.785

Gnomad4 EAS AF: 0.361

Gnomad4 SAS AF: 0.600

Gnomad4 FIN AF: 0.792

Gnomad4 NFE AF: 0.821

Gnomad4 OTH AF: 0.646

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 v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11631385; hg19: chr15-48608083;