rs181553

Variant names:

• chr18-49035660-G-A
• rs181553
• ENST00000584252.1:n.243-4340G>A

Variant summary

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

The ENST00000584252.1(DYM-AS1):​n.243-4340G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.535 in 151,746 control chromosomes in the GnomAD database, including 24,803 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 0.54 (24803 hom., cov: 31)
• Consequence: DYM-AS1 ENST00000584252.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.616
• Publications: 9 publications found

Genes affected

DYM-AS1 (HGNC:37046): (DYM antisense RNA 1)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.6).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.678 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000584252.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DYM-AS1	NR_148999.1		n.243-4340G>A		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DYM-AS1	ENST00000584252.1	TSL:5	n.243-4340G>A		intron	N/A
	DYM-AS1	ENST00000839911.1		n.381-4340G>A		intron	N/A
	DYM-AS1	ENST00000839912.1		n.381+9507G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.535 AC: 81193 AN: 151628 Hom.: 24795 Cov.: 31

Gnomad AFR AF: 0.241

Gnomad AMI AF: 0.660

Gnomad AMR AF: 0.673

Gnomad ASJ AF: 0.708

Gnomad EAS AF: 0.290

Gnomad SAS AF: 0.407

Gnomad FIN AF: 0.632

Gnomad MID AF: 0.627

Gnomad NFE AF: 0.683

Gnomad OTH AF: 0.604

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

GnomAD4 genome AF: 0.535 AC: 81218 AN: 151746 Hom.: 24803 Cov.: 31 AF XY: 0.533 AC XY: 39485 AN XY: 74110

African (AFR) AF: 0.241 AC: 9968 AN: 41324

American (AMR) AF: 0.673 AC: 10272 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.708 AC: 2456 AN: 3468

East Asian (EAS) AF: 0.290 AC: 1497 AN: 5168

South Asian (SAS) AF: 0.410 AC: 1966 AN: 4800

European-Finnish (FIN) AF: 0.632 AC: 6627 AN: 10486

Middle Eastern (MID) AF: 0.619 AC: 182 AN: 294

European-Non Finnish (NFE) AF: 0.683 AC: 46393 AN: 67930

Other (OTH) AF: 0.598 AC: 1259 AN: 2106

Alfa AF: 0.642 Hom.: 26968

Bravo AF: 0.528

Asia WGS AF: 0.333 AC: 1157 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.60
CADD	Benign	7.4
DANN	Benign	0.96
PhyloP100		0.62

Splicing

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

Other links and lift over

dbSNP: rs181553; hg19: chr18-46562030;