rs580036

Variant names:

• chr18-67868810-C-A
• rs580036
• ENST00000583687.1:n.382-5277C>A

Your query was ambiguous. Multiple possible variants found:

• chr18-67868810-C-A
• chr18-67868810-C-G
• chr18-67868810-C-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.382-5277C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.555 in 151,882 control chromosomes in the GnomAD database, including 25,607 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 0.56 (25607 hom., cov: 31)
• Consequence: DSEL-AS1 ENST00000583687.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.711
• Publications: 1 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=-0.95).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.666 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DSEL-AS1	NR_033921.1	n.382-5277C>A		intron_variant	Intron 3 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DSEL-AS1	ENST00000583687.1	n.382-5277C>A		intron_variant	Intron 3 of 4	1

Frequencies

GnomAD3 genomes AF: 0.555 AC: 84296 AN: 151764 Hom.: 25595 Cov.: 31

Gnomad AFR AF: 0.292

Gnomad AMI AF: 0.761

Gnomad AMR AF: 0.637

Gnomad ASJ AF: 0.645

Gnomad EAS AF: 0.465

Gnomad SAS AF: 0.602

Gnomad FIN AF: 0.697

Gnomad MID AF: 0.608

Gnomad NFE AF: 0.671

Gnomad OTH AF: 0.559

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

GnomAD4 genome AF: 0.555 AC: 84344 AN: 151882 Hom.: 25607 Cov.: 31 AF XY: 0.559 AC XY: 41483 AN XY: 74230

African (AFR) AF: 0.293 AC: 12124 AN: 41424

American (AMR) AF: 0.637 AC: 9698 AN: 15228

Ashkenazi Jewish (ASJ) AF: 0.645 AC: 2239 AN: 3470

East Asian (EAS) AF: 0.464 AC: 2388 AN: 5146

South Asian (SAS) AF: 0.603 AC: 2905 AN: 4818

European-Finnish (FIN) AF: 0.697 AC: 7352 AN: 10546

Middle Eastern (MID) AF: 0.609 AC: 179 AN: 294

European-Non Finnish (NFE) AF: 0.671 AC: 45591 AN: 67942

Other (OTH) AF: 0.559 AC: 1177 AN: 2106

Alfa AF: 0.594 Hom.: 4161

Bravo AF: 0.547

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	2.4
DANN	Benign	0.33
PhyloP100		0.71

Splicing

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

Other links and lift over

dbSNP: rs580036; hg19: chr18-65536047;