Variant chr7-151381679-A-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2

The NM_198285.3(WDR86):c.1034T>G(p.Leu345Arg) variant causes a missense change. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Uncertain significance (★).

Frequency

Genomes: not found (cov: 34)

Exomes 𝑓: 0.0000016 ( 0 hom. )

Failed GnomAD Quality Control

Consequence

WDR86
NM_198285.3 missense

Scores

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 4.21

Variant links:

Genes affected

WDR86 (HGNC:28020): (WD repeat domain 86)

WDR86 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 2 ACMG points.

PM2

Very rare variant in population databases, with high coverage;

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
WDR86	NM_198285.3 linkuse as main transcript	c.1034T>G	p.Leu345Arg	missense_variant	6/6	ENST00000334493.11

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
WDR86	ENST00000334493.11 linkuse as main transcript	c.1034T>G	p.Leu345Arg	missense_variant	6/6	5	NM_198285.3	P1	Q86TI4-3

Frequencies

GnomAD3 genomes

Cov.:

GnomAD4 exome

Data not reliable, filtered out with message: AS_VQSR

AF:

0.00000157

AC:

AN:

1277502

Hom.:

Cov.:

AF XY:

0.00000160

AC XY:

AN XY:

625614

show subpopulations

Gnomad4 AFR exome

AF:

0.00

Gnomad4 AMR exome

AF:

0.00

Gnomad4 ASJ exome

AF:

0.00

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.00

Gnomad4 FIN exome

AF:

0.00

Gnomad4 NFE exome

AF:

0.00000194

Gnomad4 OTH exome

AF:

0.00

GnomAD4 genome

Cov.:

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not specified

Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

Ambry Genetics

Dec 13, 2022

The c.1034T>G (p.L345R) alteration is located in exon 6 (coding exon 6) of the WDR86 gene. This alteration results from a T to G substitution at nucleotide position 1034, causing the leucine (L) at amino acid position 345 to be replaced by an arginine (R). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.20

BayesDel_addAF

Benign

-0.0056

BayesDel_noAF

Benign

-0.25

CADD

Benign

DANN

Uncertain

0.98

DEOGEN2

Benign

0.011

T;.

Eigen

Benign

0.11

Eigen_PC

Benign

0.055

FATHMM_MKL

Benign

0.58

LIST_S2

Benign

0.49

T;T

M_CAP

Pathogenic

0.76

MetaRNN

Uncertain

0.46

T;T

MetaSVM

Benign

-0.93

MutationTaster

Benign

0.96

D;D;N

PrimateAI

Pathogenic

0.81

PROVEAN

Uncertain

-2.6

D;.

REVEL

Benign

0.27

Sift

Uncertain

0.0010

D;.

Sift4G

Uncertain

0.020

D;D

Polyphen

0.92

P;.

Vest4

0.18

MutPred

0.53

Gain of disorder (P = 0.0123);.;

MVP

0.42

MPC

1.4

ClinPred

0.97

GERP RS

4.5

Varity_R

0.61

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

No publications associated with this variant yet.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

Other links and lift over