rs6705628

Positions:

• chr2-73981235-C-T

Variant summary

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

The NR_104030.1(DGUOK-AS1):​n.205G>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.103 in 152,228 control chromosomes in the GnomAD database, including 2,052 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 (2052 hom., cov: 32)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: DGUOK-AS1 NR_104030.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.30

Genes affected

DGUOK-AS1 (HGNC:43441): (DGUOK antisense RNA 1)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.292 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
DGUOK-AS1	NR_104030.1	n.205G>A		non_coding_transcript_exon_variant	1/2
DGUOK-AS1	NR_104029.1	n.205G>A		non_coding_transcript_exon_variant	1/2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
DGUOK-AS1	ENST00000667561.3	n.207G>A		non_coding_transcript_exon_variant	1/2

Frequencies

GnomAD3 genomes AF: 0.103 AC: 15686 AN: 152110 Hom.: 2046 Cov.: 32

Gnomad AFR AF: 0.296

Gnomad AMI AF: 0.0121

Gnomad AMR AF: 0.0718

Gnomad ASJ AF: 0.00893

Gnomad EAS AF: 0.161

Gnomad SAS AF: 0.0374

Gnomad FIN AF: 0.00725

Gnomad MID AF: 0.0253

Gnomad NFE AF: 0.0154

Gnomad OTH AF: 0.0675

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 30 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 20

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.00

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome AF: 0.103 AC: 15709 AN: 152228 Hom.: 2052 Cov.: 32 AF XY: 0.101 AC XY: 7499 AN XY: 74412

Gnomad4 AFR AF: 0.296

Gnomad4 AMR AF: 0.0715

Gnomad4 ASJ AF: 0.00893

Gnomad4 EAS AF: 0.161

Gnomad4 SAS AF: 0.0375

Gnomad4 FIN AF: 0.00725

Gnomad4 NFE AF: 0.0154

Gnomad4 OTH AF: 0.0664

Alfa AF: 0.0388 Hom.: 241

Bravo AF: 0.119

Asia WGS AF: 0.0960 AC: 335 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	1.4
DANN	Benign	0.78

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6705628; hg19: chr2-74208362;