rs17827708

Positions:

• chr18-67622458-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.204+105709A>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 0.118 in 152,202 control chromosomes in the GnomAD database, including 1,216 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 0.12 (1216 hom., cov: 32)
• Consequence: DSEL-AS1 NR_033921.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.112

Genes affected

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

LOC105372174 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.145 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
DSEL-AS1	NR_033921.1	n.204+105709A>G		intron_variant, non_coding_transcript_variant
LOC105372174	XR_935590.3	n.105+1330T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
DSEL-AS1	ENST00000583687.1	n.204+105709A>G		intron_variant, non_coding_transcript_variant		1

Frequencies

GnomAD3 genomes AF: 0.118 AC: 17993 AN: 152084 Hom.: 1219 Cov.: 32

Gnomad AFR AF: 0.0677

Gnomad AMI AF: 0.138

Gnomad AMR AF: 0.0966

Gnomad ASJ AF: 0.294

Gnomad EAS AF: 0.0129

Gnomad SAS AF: 0.119

Gnomad FIN AF: 0.145

Gnomad MID AF: 0.218

Gnomad NFE AF: 0.147

Gnomad OTH AF: 0.147

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

GnomAD4 genome AF: 0.118 AC: 17992 AN: 152202 Hom.: 1216 Cov.: 32 AF XY: 0.118 AC XY: 8787 AN XY: 74396

Gnomad4 AFR AF: 0.0678

Gnomad4 AMR AF: 0.0963

Gnomad4 ASJ AF: 0.294

Gnomad4 EAS AF: 0.0129

Gnomad4 SAS AF: 0.120

Gnomad4 FIN AF: 0.145

Gnomad4 NFE AF: 0.147

Gnomad4 OTH AF: 0.144

Alfa AF: 0.131 Hom.: 566

Bravo AF: 0.112

Asia WGS AF: 0.0700 AC: 244 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	3.6
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: rs17827708; hg19: chr18-65289695;