rs9966483

Variant names:

• chr18-67783109-G-A
• rs9966483
• ENST00000583687.1:n.205-51310G>A

Your query was ambiguous. Multiple possible variants found:

• chr18-67783109-G-A
• chr18-67783109-G-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000583687.1(DSEL-AS1):​n.205-51310G>A variant causes a intron 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 ENST00000583687.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.124
• Publications: 3 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
DSEL-AS1	NR_033921.1	n.205-51310G>A		intron_variant	Intron 1 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DSEL-AS1	ENST00000583687.1	n.205-51310G>A		intron_variant	Intron 1 of 4	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

African (AFR) AF: 0.370 AC: 15299 AN: 41384

American (AMR) AF: 0.180 AC: 2734 AN: 15222

Ashkenazi Jewish (ASJ) AF: 0.214 AC: 740 AN: 3456

East Asian (EAS) AF: 0.120 AC: 620 AN: 5168

South Asian (SAS) AF: 0.190 AC: 916 AN: 4822

European-Finnish (FIN) AF: 0.138 AC: 1466 AN: 10588

Middle Eastern (MID) AF: 0.180 AC: 53 AN: 294

European-Non Finnish (NFE) AF: 0.212 AC: 14326 AN: 67726

Other (OTH) AF: 0.251 AC: 530 AN: 2112

Alfa AF: 0.111 Hom.: 181

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
PhyloP100		-0.12

Splicing

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

Other links and lift over

dbSNP: rs9966483; hg19: chr18-65450346;