rs1667216

Positions:

• chr18-31549968-G-A
• chr18-31549968-G-C
• chr18-31549968-G-T

Variant summary

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

The NR_045216.1(DSG2-AS1):​n.1345+70C>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 0.506 in 152,022 control chromosomes in the GnomAD database, including 21,864 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 0.51 (21864 hom., cov: 32)
  • Exomes 𝑓: 0.25 (0 hom.)
• Consequence: DSG2-AS1 NR_045216.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.626

Genes affected

DSG2-AS1 (HGNC:51311): (DSG2 antisense RNA 1)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.767 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
DSG2-AS1	NR_045216.1	n.1345+70C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
DSG2-AS1	ENST00000583706.5	n.1383+70C>T		intron_variant, non_coding_transcript_variant		5
DSG2-AS1	ENST00000657343.1	n.696+70C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.505 AC: 76771 AN: 151896 Hom.: 21815 Cov.: 32

Gnomad AFR AF: 0.774

Gnomad AMI AF: 0.311

Gnomad AMR AF: 0.452

Gnomad ASJ AF: 0.331

Gnomad EAS AF: 0.710

Gnomad SAS AF: 0.344

Gnomad FIN AF: 0.407

Gnomad MID AF: 0.408

Gnomad NFE AF: 0.378

Gnomad OTH AF: 0.468

GnomAD4 exome AF: 0.250 AC: 2 AN: 8 Hom.: 0 AF XY: 0.250 AC XY: 2 AN XY: 8

Gnomad4 FIN exome AF: 0.250

Gnomad4 NFE exome AF: 0.250

GnomAD4 genome AF: 0.506 AC: 76883 AN: 152014 Hom.: 21864 Cov.: 32 AF XY: 0.505 AC XY: 37515 AN XY: 74310

Gnomad4 AFR AF: 0.775

Gnomad4 AMR AF: 0.452

Gnomad4 ASJ AF: 0.331

Gnomad4 EAS AF: 0.710

Gnomad4 SAS AF: 0.342

Gnomad4 FIN AF: 0.407

Gnomad4 NFE AF: 0.378

Gnomad4 OTH AF: 0.473

Alfa AF: 0.398 Hom.: 6130

Bravo AF: 0.523

Asia WGS AF: 0.571 AC: 1986 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.2
DANN	Benign	0.37

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1667216; hg19: chr18-29129931;