rs114535501

Variant names:

• chr18-67803512-A-G
• rs114535501
• ENST00000583687.1:n.205-30907A>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.205-30907A>G variant causes a intron 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 ENST00000583687.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0880
• Publications: 1 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
DSEL-AS1	NR_033921.1	n.205-30907A>G		intron_variant	Intron 1 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DSEL-AS1	ENST00000583687.1	n.205-30907A>G		intron_variant	Intron 1 of 4	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

African (AFR) AF: 0.197 AC: 8170 AN: 41426

American (AMR) AF: 0.0740 AC: 1127 AN: 15236

Ashkenazi Jewish (ASJ) AF: 0.218 AC: 757 AN: 3468

East Asian (EAS) AF: 0.112 AC: 577 AN: 5172

South Asian (SAS) AF: 0.0746 AC: 360 AN: 4824

European-Finnish (FIN) AF: 0.0125 AC: 132 AN: 10598

Middle Eastern (MID) AF: 0.153 AC: 45 AN: 294

European-Non Finnish (NFE) AF: 0.0583 AC: 3963 AN: 67998

Other (OTH) AF: 0.109 AC: 231 AN: 2116

Alfa AF: 0.0842 Hom.: 104

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
PhyloP100		-0.088

Splicing

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

Other links and lift over

dbSNP: rs114535501; hg19: chr18-65470749;