rs181553

Positions:

• chr18-49035660-G-A

Variant summary

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

The NR_148999.1(DYM-AS1):​n.243-4340G>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 0.535 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 NR_148999.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.616

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
DYM-AS1	NR_148999.1	n.243-4340G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
DYM-AS1	ENST00000584252.1	n.243-4340G>A		intron_variant, non_coding_transcript_variant		5

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

Gnomad4 AFR AF: 0.241

Gnomad4 AMR AF: 0.673

Gnomad4 ASJ AF: 0.708

Gnomad4 EAS AF: 0.290

Gnomad4 SAS AF: 0.410

Gnomad4 FIN AF: 0.632

Gnomad4 NFE AF: 0.683

Gnomad4 OTH AF: 0.598

Alfa AF: 0.631 Hom.: 18244

Bravo AF: 0.528

Asia WGS AF: 0.333 AC: 1157 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs181553; hg19: chr18-46562030;