rs13353224

Variant names:

• chr18-67733188-A-G
• rs13353224
• ENST00000583687.1:n.205-101231A>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.205-101231A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0743 in 152,138 control chromosomes in the GnomAD database, including 497 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 0.074 (497 hom., cov: 31)
• Consequence: DSEL-AS1 ENST00000583687.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0510
• Publications: 6 publications found

Genes affected

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

ENSG00000263594 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.126 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DSEL-AS1	NR_033921.1	n.205-101231A>G		intron_variant	Intron 1 of 4
LOC105372173	NR_188049.1	n.44+33820T>C		intron_variant	Intron 1 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DSEL-AS1	ENST00000583687.1	n.205-101231A>G		intron_variant	Intron 1 of 4	1
ENSG00000263594	ENST00000666895.2	n.54+33820T>C		intron_variant	Intron 1 of 3
ENSG00000263594	ENST00000782046.1	n.111+15480T>C		intron_variant	Intron 2 of 5

Frequencies

GnomAD3 genomes AF: 0.0741 AC: 11271 AN: 152020 Hom.: 494 Cov.: 31

Gnomad AFR AF: 0.128

Gnomad AMI AF: 0.0735

Gnomad AMR AF: 0.0557

Gnomad ASJ AF: 0.0760

Gnomad EAS AF: 0.000388

Gnomad SAS AF: 0.0243

Gnomad FIN AF: 0.0261

Gnomad MID AF: 0.0506

Gnomad NFE AF: 0.0619

Gnomad OTH AF: 0.0779

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

GnomAD4 genome AF: 0.0743 AC: 11299 AN: 152138 Hom.: 497 Cov.: 31 AF XY: 0.0706 AC XY: 5250 AN XY: 74390

African (AFR) AF: 0.129 AC: 5332 AN: 41466

American (AMR) AF: 0.0556 AC: 849 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.0760 AC: 264 AN: 3472

East Asian (EAS) AF: 0.000389 AC: 2 AN: 5148

South Asian (SAS) AF: 0.0245 AC: 118 AN: 4818

European-Finnish (FIN) AF: 0.0261 AC: 277 AN: 10616

Middle Eastern (MID) AF: 0.0544 AC: 16 AN: 294

European-Non Finnish (NFE) AF: 0.0619 AC: 4212 AN: 68024

Other (OTH) AF: 0.0766 AC: 162 AN: 2114

Alfa AF: 0.0679 Hom.: 934

Bravo AF: 0.0797

Asia WGS AF: 0.0150 AC: 51 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.82
DANN	Benign	0.40
PhyloP100		-0.051
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs13353224; hg19: chr18-65400425;