10-120851534-A-G

Variant names:

• chr10-120851534-A-G
• rs78163411
• NM_018117.12:c.86+28A>G

Variant summary

Our verdict is Benign. The variant received -20 ACMG points: 0P and 20B. BP4_Strong BP6_Very_Strong BS1 BS2

The NM_018117.12(WDR11):​c.86+28A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00187 in 1,599,742 control chromosomes in the GnomAD database, including 42 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).

• Frequency:
  • Genomes: 𝑓 0.010 (23 hom., cov: 33)
  • Exomes 𝑓: 0.00096 (19 hom.)
• Consequence: WDR11 NM_018117.12 intron
• Clinical Significance: Likely benign criteria provided, multiple submitters, no conflicts B:2
• Conservation: PhyloP100: -0.132

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-DT (HGNC:27437): (WDR11 divergent transcript)

ACMG classification

Our verdict: Benign. The variant received -20 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.74).
• BP6: Variant 10-120851534-A-G is Benign according to our data. Variant chr10-120851534-A-G is described in ClinVar as [Likely_benign]. Clinvar id is 1219686.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BS1: Variant frequency is greater than expected in population afr. GnomAd4 allele frequency = 0.0105 (1596/152308) while in subpopulation AFR AF = 0.0366 (1523/41570). AF 95% confidence interval is 0.0351. There are 23 homozygotes in GnomAd4. There are 775 alleles in the male GnomAd4 subpopulation. Median coverage is 33. This position FAILED quality control check.
• BS2: High AC in GnomAd4 at 1596 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
WDR11	NM_018117.12	c.86+28A>G		intron_variant	Intron 1 of 28	ENST00000263461.11	NP_060587.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
WDR11	ENST00000263461.11	c.86+28A>G		intron_variant	Intron 1 of 28	1	NM_018117.12	ENSP00000263461.5
WDR11	ENST00000605543.5	n.86+28A>G		intron_variant	Intron 1 of 21	2		ENSP00000475076.1

Frequencies

GnomAD3 genomes AF: 0.0105 AC: 1595 AN: 152190 Hom.: 23 Cov.: 33

Gnomad AFR AF: 0.0367

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00334

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.000207

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00633

Gnomad NFE AF: 0.0000441

Gnomad OTH AF: 0.00764

GnomAD2 exomes AF: 0.00234 AC: 504 AN: 215192 AF XY: 0.00178

Gnomad AFR exome AF: 0.0365

Gnomad AMR exome AF: 0.00109

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.00

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.0000317

Gnomad OTH exome AF: 0.000552

GnomAD4 exome AF: 0.000963 AC: 1394 AN: 1447434 Hom.: 19 Cov.: 31 AF XY: 0.000774 AC XY: 556 AN XY: 718560

Gnomad4 AFR exome AF: 0.0363 AC: 1214 AN: 33398

Gnomad4 AMR exome AF: 0.00120 AC: 51 AN: 42342

Gnomad4 ASJ exome AF: 0.00 AC: 0 AN: 25744

Gnomad4 EAS exome AF: 0.00 AC: 0 AN: 39298

Gnomad4 SAS exome AF: 0.0000358 AC: 3 AN: 83718

Gnomad4 FIN exome AF: 0.00 AC: 0 AN: 50874

Gnomad4 NFE exome AF: 0.00000994 AC: 11 AN: 1106392

Gnomad4 Remaining exome AF: 0.00185 AC: 111 AN: 59912

GnomAD4 genome AF: 0.0105 AC: 1596 AN: 152308 Hom.: 23 Cov.: 33 AF XY: 0.0104 AC XY: 775 AN XY: 74474

Gnomad4 AFR AF: 0.0366 AC: 0.036637 AN: 0.036637

Gnomad4 AMR AF: 0.00333 AC: 0.00333246 AN: 0.00333246

Gnomad4 ASJ AF: 0.00 AC: 0 AN: 0

Gnomad4 EAS AF: 0.00 AC: 0 AN: 0

Gnomad4 SAS AF: 0.000207 AC: 0.000207125 AN: 0.000207125

Gnomad4 FIN AF: 0.00 AC: 0 AN: 0

Gnomad4 NFE AF: 0.0000441 AC: 0.0000441099 AN: 0.0000441099

Gnomad4 OTH AF: 0.00756 AC: 0.00756144 AN: 0.00756144

Alfa AF: 0.0114 Hom.: 11

Bravo AF: 0.0113

Asia WGS AF: 0.000866 AC: 3 AN: 3478

ClinVar

Significance: Likely benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

not provided Benign:2

-

Breakthrough Genomics, Breakthrough Genomics

Significance: Likely benign

Review Status: criteria provided, single submitter

Collection Method: not provided

- -

Nov 27, 2018

GeneDx

Significance: Likely 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	-0.74
CADD	Benign	5.1
DANN	Benign	0.80
Mutation Taster		=100/0	polymorphism

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: rs78163411; hg19: chr10-122611046;