rs114535501

Positions:

• chr18-67803512-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.205-30907A>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 0.101 in 152,044 control chromosomes in the GnomAD database, including 1,074 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 0.10 (1074 hom., cov: 32)
• Consequence: DSEL-AS1 NR_033921.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0880

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=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.194 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
DSEL-AS1	NR_033921.1	n.205-30907A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
DSEL-AS1	ENST00000583687.1	n.205-30907A>G		intron_variant, non_coding_transcript_variant		1

Frequencies

GnomAD3 genomes AF: 0.101 AC: 15365 AN: 151926 Hom.: 1069 Cov.: 32

Gnomad AFR AF: 0.197

Gnomad AMI AF: 0.0384

Gnomad AMR AF: 0.0741

Gnomad ASJ AF: 0.218

Gnomad EAS AF: 0.111

Gnomad SAS AF: 0.0750

Gnomad FIN AF: 0.0125

Gnomad MID AF: 0.161

Gnomad NFE AF: 0.0583

Gnomad OTH AF: 0.109

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

GnomAD4 genome AF: 0.101 AC: 15397 AN: 152044 Hom.: 1074 Cov.: 32 AF XY: 0.0991 AC XY: 7368 AN XY: 74320

Gnomad4 AFR AF: 0.197

Gnomad4 AMR AF: 0.0740

Gnomad4 ASJ AF: 0.218

Gnomad4 EAS AF: 0.112

Gnomad4 SAS AF: 0.0746

Gnomad4 FIN AF: 0.0125

Gnomad4 NFE AF: 0.0583

Gnomad4 OTH AF: 0.109

Alfa AF: 0.0805 Hom.: 85

Bravo AF: 0.109

Asia WGS AF: 0.0850 AC: 294 AN: 3460

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	4.4
DANN	Benign	0.84

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs114535501; hg19: chr18-65470749;