rs6705628

Variant names:

• chr2-73981235-C-T
• rs6705628
• ENST00000413452.4:n.523G>A

Variant summary

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

The ENST00000413452.4(DGUOK-AS1):​n.523G>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 ENST00000413452.4 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.30
• Publications: 23 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
DGUOK-AS1	NR_104029.1	n.205G>A		non_coding_transcript_exon_variant	Exon 1 of 2
DGUOK-AS1	NR_104030.1	n.205G>A		non_coding_transcript_exon_variant	Exon 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DGUOK-AS1	ENST00000413452.4	n.523G>A		non_coding_transcript_exon_variant	Exon 1 of 2	3
DGUOK-AS1	ENST00000439192.4	n.520G>A		non_coding_transcript_exon_variant	Exon 1 of 2	2
DGUOK-AS1	ENST00000453103.1	n.207G>A		non_coding_transcript_exon_variant	Exon 1 of 2	3

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

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 4

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 22

Other (OTH) AF: 0.00 AC: 0 AN: 4

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

African (AFR) AF: 0.296 AC: 12285 AN: 41492

American (AMR) AF: 0.0715 AC: 1094 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.00893 AC: 31 AN: 3470

East Asian (EAS) AF: 0.161 AC: 835 AN: 5184

South Asian (SAS) AF: 0.0375 AC: 181 AN: 4830

European-Finnish (FIN) AF: 0.00725 AC: 77 AN: 10622

Middle Eastern (MID) AF: 0.0272 AC: 8 AN: 294

European-Non Finnish (NFE) AF: 0.0154 AC: 1047 AN: 68016

Other (OTH) AF: 0.0664 AC: 140 AN: 2110

Alfa AF: 0.0508 Hom.: 1526

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
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs6705628; hg19: chr2-74208362;