rs13353224

chr18-67733188-A-G

Variant summary

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

The NR_033921.1(DSEL-AS1):n.205-101231A>G 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 0.0743 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 NR_033921.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0510

Genes affected

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

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
DSEL-AS1	NR_033921.1	n.205-101231A>G		intron_variant, non_coding_transcript_variant
LOC105372173	XR_007066408.1	n.202+33820T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
DSEL-AS1	ENST00000583687.1	n.205-101231A>G		intron_variant, non_coding_transcript_variant		1
	ENST00000666895.1	n.44+33820T>C		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.129

Gnomad4 AMR AF: 0.0556

Gnomad4 ASJ AF: 0.0760

Gnomad4 EAS AF: 0.000389

Gnomad4 SAS AF: 0.0245

Gnomad4 FIN AF: 0.0261

Gnomad4 NFE AF: 0.0619

Gnomad4 OTH AF: 0.0766

Alfa AF: 0.0643 Hom.: 567

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13353224; hg19: chr18-65400425;