18-67928681-T-C

Variant names:

• chr18-67928681-T-C
• rs726523
• ENST00000757632.1:n.665-826T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000757632.1(DSEL-AS1):​n.665-826T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.622 in 151,948 control chromosomes in the GnomAD database, including 31,577 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 0.62 (31577 hom., cov: 32)
• Consequence: DSEL-AS1 ENST00000757632.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00100
• Publications: 4 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=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.739 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DSEL-AS1	ENST00000757632.1	n.665-826T>C		intron_variant	Intron 4 of 4

Frequencies

GnomAD3 genomes AF: 0.623 AC: 94537 AN: 151830 Hom.: 31578 Cov.: 32

Gnomad AFR AF: 0.348

Gnomad AMI AF: 0.773

Gnomad AMR AF: 0.690

Gnomad ASJ AF: 0.627

Gnomad EAS AF: 0.657

Gnomad SAS AF: 0.745

Gnomad FIN AF: 0.726

Gnomad MID AF: 0.675

Gnomad NFE AF: 0.745

Gnomad OTH AF: 0.643

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

GnomAD4 genome AF: 0.622 AC: 94541 AN: 151948 Hom.: 31577 Cov.: 32 AF XY: 0.625 AC XY: 46388 AN XY: 74264

African (AFR) AF: 0.347 AC: 14393 AN: 41464

American (AMR) AF: 0.689 AC: 10516 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.627 AC: 2174 AN: 3470

East Asian (EAS) AF: 0.657 AC: 3390 AN: 5158

South Asian (SAS) AF: 0.745 AC: 3591 AN: 4820

European-Finnish (FIN) AF: 0.726 AC: 7665 AN: 10562

Middle Eastern (MID) AF: 0.671 AC: 196 AN: 292

European-Non Finnish (NFE) AF: 0.745 AC: 50570 AN: 67908

Other (OTH) AF: 0.636 AC: 1341 AN: 2108

Alfa AF: 0.698 Hom.: 45240

Bravo AF: 0.609

Asia WGS AF: 0.654 AC: 2251 AN: 3446

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.3
DANN	Benign	0.72
PhyloP100		-0.0010

Splicing

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

Other links and lift over

dbSNP: rs726523; hg19: chr18-65595918;