18-67804281-C-T

Position:

• chr18-67804281-C-T

Variant summary

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

The ENST00000583687.1(DSEL-AS1):​n.205-30138C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0452 in 152,236 control chromosomes in the GnomAD database, including 212 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 (212 hom., cov: 32)
• Consequence: DSEL-AS1 ENST00000583687.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.98

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=-0.95).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.051 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
DSEL-AS1	NR_033921.1	n.205-30138C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
DSEL-AS1	ENST00000583687.1	n.205-30138C>T		intron_variant		1

Frequencies

GnomAD3 genomes AF: 0.0451 AC: 6867 AN: 152118 Hom.: 211 Cov.: 32

Gnomad AFR AF: 0.0344

Gnomad AMI AF: 0.0374

Gnomad AMR AF: 0.0507

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: 0.0524

Gnomad OTH AF: 0.0641

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

GnomAD4 genome AF: 0.0452 AC: 6875 AN: 152236 Hom.: 212 Cov.: 32 AF XY: 0.0430 AC XY: 3204 AN XY: 74434

Gnomad4 AFR AF: 0.0346

Gnomad4 AMR AF: 0.0506

Gnomad4 ASJ AF: 0.191

Gnomad4 EAS AF: 0.000193

Gnomad4 SAS AF: 0.0209

Gnomad4 FIN AF: 0.0123

Gnomad4 NFE AF: 0.0524

Gnomad4 OTH AF: 0.0639

Alfa AF: 0.0320 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	-0.95
CADD	Benign	0.77
DANN	Benign	0.74

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs74789784; hg19: chr18-65471518;