ENST00000583687.1:n.205-17844C>G

Variant names:

• chr18-67816575-C-G
• rs11661646
• ENST00000583687.1:n.205-17844C>G

Variant summary

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

The ENST00000583687.1(DSEL-AS1):​n.205-17844C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0385 in 152,060 control chromosomes in the GnomAD database, including 190 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 0.038 (190 hom., cov: 32)
• Consequence: DSEL-AS1 ENST00000583687.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.212
• Publications: 2 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=-0.83).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0511 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000583687.1. 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
	DSEL-AS1	NR_033921.1		n.205-17844C>G		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DSEL-AS1	ENST00000583687.1	TSL:1	n.205-17844C>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0385 AC: 5845 AN: 151942 Hom.: 189 Cov.: 32

Gnomad AFR AF: 0.0122

Gnomad AMI AF: 0.0373

Gnomad AMR AF: 0.0455

Gnomad ASJ AF: 0.188

Gnomad EAS AF: 0.000193

Gnomad SAS AF: 0.0203

Gnomad FIN AF: 0.0126

Gnomad MID AF: 0.123

Gnomad NFE AF: 0.0525

Gnomad OTH AF: 0.0580

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

GnomAD4 genome AF: 0.0385 AC: 5850 AN: 152060 Hom.: 190 Cov.: 32 AF XY: 0.0369 AC XY: 2745 AN XY: 74338

African (AFR) AF: 0.0125 AC: 517 AN: 41512

American (AMR) AF: 0.0454 AC: 693 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.188 AC: 652 AN: 3468

East Asian (EAS) AF: 0.000193 AC: 1 AN: 5168

South Asian (SAS) AF: 0.0201 AC: 97 AN: 4814

European-Finnish (FIN) AF: 0.0126 AC: 133 AN: 10592

Middle Eastern (MID) AF: 0.119 AC: 35 AN: 294

European-Non Finnish (NFE) AF: 0.0525 AC: 3566 AN: 67928

Other (OTH) AF: 0.0579 AC: 122 AN: 2108

Alfa AF: 0.0454 Hom.: 23

Bravo AF: 0.0391

Asia WGS AF: 0.0150 AC: 52 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	1.6
DANN	Benign	0.72
PhyloP100		0.21

Splicing

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

Other links and lift over

dbSNP: rs11661646; hg19: chr18-65483812;