rs9966483

chr18-67783109-G-Achr18-67783109-G-T

Variant summary

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

The NR_033921.1(DSEL-AS1):n.205-51310G>A 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 0.243 in 151,684 control chromosomes in the GnomAD database, including 5,018 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 0.24 (5018 hom., cov: 32)
• Consequence: DSEL-AS1 NR_033921.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.124

Genes affected

DSEL-AS1 (HGNC:55325): (DSEL antisense RNA 1)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.365 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
DSEL-AS1	NR_033921.1	n.205-51310G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
DSEL-AS1	ENST00000583687.1	n.205-51310G>A		intron_variant, non_coding_transcript_variant		1

Frequencies

GnomAD3 genomes AF: 0.243 AC: 36885 AN: 151566 Hom.: 5010 Cov.: 32

Gnomad AFR AF: 0.370

Gnomad AMI AF: 0.247

Gnomad AMR AF: 0.180

Gnomad ASJ AF: 0.214

Gnomad EAS AF: 0.120

Gnomad SAS AF: 0.189

Gnomad FIN AF: 0.138

Gnomad MID AF: 0.187

Gnomad NFE AF: 0.212

Gnomad OTH AF: 0.248

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

GnomAD4 genome AF: 0.243 AC: 36909 AN: 151684 Hom.: 5018 Cov.: 32 AF XY: 0.236 AC XY: 17520 AN XY: 74166

Gnomad4 AFR AF: 0.370

Gnomad4 AMR AF: 0.180

Gnomad4 ASJ AF: 0.214

Gnomad4 EAS AF: 0.120

Gnomad4 SAS AF: 0.190

Gnomad4 FIN AF: 0.138

Gnomad4 NFE AF: 0.212

Gnomad4 OTH AF: 0.251

Alfa AF: 0.0985 Hom.: 134

Bravo AF: 0.253

Asia WGS AF: 0.168 AC: 586 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	2.4
Dann	Benign	0.43

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9966483; hg19: chr18-65450346;