2-159252747-C-G

Variant names:

• chr2-159252747-C-G
• rs10490002
• NM_001128212.3:c.1132+3449G>C

Variant summary

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

The NM_001128212.3(WDSUB1):​c.1132+3449G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.27 in 152,028 control chromosomes in the GnomAD database, including 7,104 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 0.27 (7104 hom., cov: 33)
• Consequence: WDSUB1 NM_001128212.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.712
• Publications: 12 publications found

Genes affected

WDSUB1 (HGNC:26697): (WD repeat, sterile alpha motif and U-box domain containing 1) Predicted to enable ubiquitin-protein transferase activity. Predicted to be involved in protein ubiquitination. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.455 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001128212.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	WDSUB1	NM_001128212.3	MANE Select	c.1132+3449G>C		intron	N/A	NP_001121684.1
	WDSUB1	NM_001128213.2		c.1132+3449G>C		intron	N/A	NP_001121685.1
	WDSUB1	NM_001330278.2		c.1132+3449G>C		intron	N/A	NP_001317207.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	WDSUB1	ENST00000359774.9	TSL:5 MANE Select	c.1132+3449G>C		intron	N/A	ENSP00000352820.4
	WDSUB1	ENST00000358147.8	TSL:1	c.856+3449G>C		intron	N/A	ENSP00000350866.4
	WDSUB1	ENST00000392796.7	TSL:2	c.1132+3449G>C		intron	N/A	ENSP00000376545.3

Frequencies

GnomAD3 genomes AF: 0.270 AC: 41026 AN: 151908 Hom.: 7095 Cov.: 33

Gnomad AFR AF: 0.0704

Gnomad AMI AF: 0.261

Gnomad AMR AF: 0.463

Gnomad ASJ AF: 0.238

Gnomad EAS AF: 0.352

Gnomad SAS AF: 0.368

Gnomad FIN AF: 0.444

Gnomad MID AF: 0.264

Gnomad NFE AF: 0.310

Gnomad OTH AF: 0.273

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

GnomAD4 genome AF: 0.270 AC: 41047 AN: 152028 Hom.: 7104 Cov.: 33 AF XY: 0.284 AC XY: 21121 AN XY: 74308

African (AFR) AF: 0.0702 AC: 2912 AN: 41478

American (AMR) AF: 0.464 AC: 7082 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.238 AC: 828 AN: 3472

East Asian (EAS) AF: 0.351 AC: 1817 AN: 5174

South Asian (SAS) AF: 0.369 AC: 1777 AN: 4816

European-Finnish (FIN) AF: 0.444 AC: 4680 AN: 10552

Middle Eastern (MID) AF: 0.264 AC: 77 AN: 292

European-Non Finnish (NFE) AF: 0.310 AC: 21062 AN: 67968

Other (OTH) AF: 0.273 AC: 575 AN: 2110

Alfa AF: 0.171 Hom.: 386

Bravo AF: 0.266

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.0
DANN	Benign	0.33
PhyloP100		-0.71
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs10490002; hg19: chr2-160109258;