chr2-73975451-T-C

Variant names:

• chr2-73975451-T-C
• rs4852324
• ENST00000413452.4:n.649+5658A>G

Variant summary

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

The ENST00000439192.4(DGUOK-AS1):​n.620+5684A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.167 in 152,214 control chromosomes in the GnomAD database, including 3,426 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 0.17 (3426 hom., cov: 32)
• Consequence: DGUOK-AS1 ENST00000439192.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.488
• Publications: 21 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=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.365 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000439192.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DGUOK-AS1	NR_104029.1		n.331+5658A>G		intron	N/A
	DGUOK-AS1	NR_104030.1		n.305+5684A>G		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DGUOK-AS1	ENST00000413452.4	TSL:3	n.649+5658A>G		intron	N/A
	DGUOK-AS1	ENST00000439192.4	TSL:2	n.620+5684A>G		intron	N/A
	DGUOK-AS1	ENST00000453103.1	TSL:3	n.307+5684A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.167 AC: 25328 AN: 152096 Hom.: 3403 Cov.: 32

Gnomad AFR AF: 0.369

Gnomad AMI AF: 0.0768

Gnomad AMR AF: 0.136

Gnomad ASJ AF: 0.0528

Gnomad EAS AF: 0.200

Gnomad SAS AF: 0.0697

Gnomad FIN AF: 0.0488

Gnomad MID AF: 0.101

Gnomad NFE AF: 0.0810

Gnomad OTH AF: 0.139

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

GnomAD4 genome AF: 0.167 AC: 25399 AN: 152214 Hom.: 3426 Cov.: 32 AF XY: 0.164 AC XY: 12207 AN XY: 74442

African (AFR) AF: 0.370 AC: 15349 AN: 41486

American (AMR) AF: 0.136 AC: 2075 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.0528 AC: 183 AN: 3466

East Asian (EAS) AF: 0.200 AC: 1036 AN: 5176

South Asian (SAS) AF: 0.0696 AC: 336 AN: 4830

European-Finnish (FIN) AF: 0.0488 AC: 518 AN: 10612

Middle Eastern (MID) AF: 0.109 AC: 32 AN: 294

European-Non Finnish (NFE) AF: 0.0810 AC: 5510 AN: 68030

Other (OTH) AF: 0.137 AC: 290 AN: 2112

Alfa AF: 0.108 Hom.: 5227

Bravo AF: 0.185

Asia WGS AF: 0.129 AC: 449 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.80
DANN	Benign	0.46
PhyloP100		-0.49

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs4852324;

hg19: chr2-74202578;