rs12306

chr17-27295085-G-T

Variant summary

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

The NM_015626.10(WSB1):c.40+650G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.331 in 152,042 control chromosomes in the GnomAD database, including 8,633 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 0.33 (8633 hom., cov: 33)
• Consequence: WSB1 NM_015626.10 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.193

Genes affected

WSB1 (HGNC:19221): (WD repeat and SOCS box containing 1) This gene encodes a member of the WD-protein subfamily. This protein shares a high sequence identity to mouse and chick proteins. It contains several WD-repeats spanning most of the protein and an SOCS box in the C-terminus. Alternatively spliced transcript variants encoding distinct isoforms have been found for this gene. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.394 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
WSB1	NM_015626.10	c.40+650G>T		intron_variant		ENST00000262394.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
WSB1	ENST00000262394.7	c.40+650G>T		intron_variant		1	NM_015626.10	P1

Frequencies

GnomAD3 genomes AF: 0.331 AC: 50303 AN: 151924 Hom.: 8630 Cov.: 33

Gnomad AFR AF: 0.240

Gnomad AMI AF: 0.546

Gnomad AMR AF: 0.367

Gnomad ASJ AF: 0.507

Gnomad EAS AF: 0.279

Gnomad SAS AF: 0.410

Gnomad FIN AF: 0.315

Gnomad MID AF: 0.437

Gnomad NFE AF: 0.366

Gnomad OTH AF: 0.368

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

GnomAD4 genome AF: 0.331 AC: 50329 AN: 152042 Hom.: 8633 Cov.: 33 AF XY: 0.331 AC XY: 24606 AN XY: 74338

Gnomad4 AFR AF: 0.240

Gnomad4 AMR AF: 0.368

Gnomad4 ASJ AF: 0.507

Gnomad4 EAS AF: 0.279

Gnomad4 SAS AF: 0.409

Gnomad4 FIN AF: 0.315

Gnomad4 NFE AF: 0.366

Gnomad4 OTH AF: 0.366

Alfa AF: 0.360 Hom.: 2435

Bravo AF: 0.332

Asia WGS AF: 0.342 AC: 1192 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
Cadd	Benign	3.2
Dann	Benign	0.34

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

Publications

LitVar

Other links and lift over

dbSNP: rs12306; hg19: chr17-25622111;