dbSNP rs7077126: WDR11:c.*71G>A (chr10-120908784-G-A) – ACMG Classification: Benign (-20 pts)

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_018117.12(WDR11):c.*71G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.352 in 1,556,868 control chromosomes in the GnomAD database, including 98,410 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.38 ( 11077 hom., cov: 32)

Exomes 𝑓: 0.35 ( 87333 hom. )

Consequence

WDR11
NM_018117.12 3_prime_UTR

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: 0.365

Variant links:

Genes affected

WDR11 (HGNC:13831): (WD repeat domain 11) This gene encodes a member of the WD repeat protein family. WD repeats are minimally conserved regions of approximately 40 amino acids typically bracketed by gly-his and trp-asp (GH-WD), which may facilitate formation of heterotrimeric or multiprotein complexes. Members of this family are involved in a variety of cellular processes, including cell cycle progression, signal transduction, apoptosis, and gene regulation. This gene is located in the chromosome 10q25-26 region, which is frequently deleted in gliomas and tumors of other tissues, and is disrupted by the t(10;19) translocation rearrangement in glioblastoma cells. The gene location suggests that it is a candidate gene for the tumor suppressor locus. [provided by RefSeq, Jul 2008]

WDR11 links:

LOC105378519 (HGNC:):

LOC105378519 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.83).

BP6

Variant 10-120908784-G-A is Benign according to our data. Variant chr10-120908784-G-A is described in ClinVar as [Benign]. Clinvar id is 1231652.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.444 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
WDR11	NM_018117.12 link	c.*71G>A		3_prime_UTR_variant	Exon 29 of 29	ENST00000263461.11	NP_060587.8	Q9BZH6

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein	UniProt
WDR11	ENST00000263461.11 link	c.*71G>A	3_prime_UTR_variant	Exon 29 of 29	1	NM_018117.12	ENSP00000263461.5	Q9BZH6
WDR11	ENST00000497136.6 link	n.*3019G>A	non_coding_transcript_exon_variant	Exon 26 of 26	1		ENSP00000474595.1	S4R3P9
WDR11	ENST00000605543.5 link	n.*2265G>A	non_coding_transcript_exon_variant	Exon 22 of 22	2		ENSP00000475076.1	S4R451
WDR11	ENST00000497136.6 link	n.*3019G>A	3_prime_UTR_variant	Exon 26 of 26	1		ENSP00000474595.1	S4R3P9
WDR11	ENST00000605543.5 link	n.*2265G>A	3_prime_UTR_variant	Exon 22 of 22	2		ENSP00000475076.1	S4R451

Frequencies

GnomAD3 genomes

AF:

0.379

AC:

57516

AN:

151792

Hom.:

11060

Cov.:

show subpopulations

Gnomad AFR

AF:

0.450

Gnomad AMI

AF:

0.379

Gnomad AMR

AF:

0.441

Gnomad ASJ

AF:

0.388

Gnomad EAS

AF:

0.417

Gnomad SAS

AF:

0.332

Gnomad FIN

AF:

0.283

Gnomad MID

AF:

0.342

Gnomad NFE

AF:

0.338

Gnomad OTH

AF:

0.370

GnomAD4 exome

AF:

0.349

AC:

490380

AN:

1404958

Hom.:

87333

Cov.:

AF XY:

0.346

AC XY:

243118

AN XY:

702492

show subpopulations

Gnomad4 AFR exome

AF:

0.439

Gnomad4 AMR exome

AF:

0.519

Gnomad4 ASJ exome

AF:

0.407

Gnomad4 EAS exome

AF:

0.386

Gnomad4 SAS exome

AF:

0.323

Gnomad4 FIN exome

AF:

0.292

Gnomad4 NFE exome

AF:

0.341

Gnomad4 OTH exome

AF:

0.359

GnomAD4 genome

AF:

0.379

AC:

57572

AN:

151910

Hom.:

11077

Cov.:

AF XY:

0.376

AC XY:

27955

AN XY:

74258

show subpopulations

Gnomad4 AFR

AF:

0.450

Gnomad4 AMR

AF:

0.441

Gnomad4 ASJ

AF:

0.388

Gnomad4 EAS

AF:

0.417

Gnomad4 SAS

AF:

0.332

Gnomad4 FIN

AF:

0.283

Gnomad4 NFE

AF:

0.338

Gnomad4 OTH

AF:

0.367

Alfa

AF:

0.347

Hom.:

8263

Bravo

AF:

0.395

Asia WGS

AF:

0.389

AC:

1355

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Breakthrough Genomics, Breakthrough Genomics

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: not provided

- -

Aug 09, 2018

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.83

CADD

Benign

4.0

DANN

Benign

0.28

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over