rs11660238

chr18-67802897-C-T

Variant summary

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

The NR_033921.1(DSEL-AS1):n.205-31522C>T 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 0.0452 in 152,156 control chromosomes in the GnomAD database, including 214 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 0.045 (214 hom., cov: 32)
• Consequence: DSEL-AS1 NR_033921.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.63

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0511 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
DSEL-AS1	NR_033921.1	n.205-31522C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
DSEL-AS1	ENST00000583687.1	n.205-31522C>T		intron_variant, non_coding_transcript_variant		1

Frequencies

GnomAD3 genomes AF: 0.0452 AC: 6869 AN: 152038 Hom.: 213 Cov.: 32

Gnomad AFR AF: 0.0343

Gnomad AMI AF: 0.0373

Gnomad AMR AF: 0.0506

Gnomad ASJ AF: 0.191

Gnomad EAS AF: 0.000193

Gnomad SAS AF: 0.0211

Gnomad FIN AF: 0.0123

Gnomad MID AF: 0.123

Gnomad NFE AF: 0.0526

Gnomad OTH AF: 0.0640

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

GnomAD4 genome AF: 0.0452 AC: 6877 AN: 152156 Hom.: 214 Cov.: 32 AF XY: 0.0430 AC XY: 3202 AN XY: 74388

Gnomad4 AFR AF: 0.0346

Gnomad4 AMR AF: 0.0505

Gnomad4 ASJ AF: 0.191

Gnomad4 EAS AF: 0.000193

Gnomad4 SAS AF: 0.0209

Gnomad4 FIN AF: 0.0123

Gnomad4 NFE AF: 0.0526

Gnomad4 OTH AF: 0.0638

Alfa AF: 0.0488 Hom.: 24

Bravo AF: 0.0467

Asia WGS AF: 0.0150 AC: 53 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	1.9
Dann	Benign	0.68

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11660238; hg19: chr18-65470134;