Genetic Variant NM_198285.3:c.1012C>G (chr7-151381701-G-C) – ACMG Classification: Uncertain_significance (1 pts)

Variant summary

Our verdict is Uncertain significance. The variant received 1 ACMG points: 2P and 1B. PM2BP4

The NM_198285.3(WDR86):c.1012C>G(p.Arg338Gly) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R338C) has been classified as Uncertain significance.

Frequency

Genomes: not found (cov: 34)

Exomes 𝑓: 0.0 ( 0 hom. )

Failed GnomAD Quality Control

Consequence

WDR86
NM_198285.3 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.567

Publications

0 publications found

Variant links:

Genes affected

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

WDR86 links:

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ACMG classification

Classification was made for transcript

Our verdict: Uncertain_significance. The variant received 1 ACMG points.

PM2

Very rare variant in population databases, with high coverage;

BP4

Computational evidence support a benign effect (MetaRNN=0.35577834).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
WDR86	NM_198285.3 link	c.1012C>G	p.Arg338Gly	missense_variant	Exon 6 of 6	ENST00000334493.11	NP_938026.2	Q86TI4-3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
WDR86	ENST00000334493.11 link	c.1012C>G	p.Arg338Gly	missense_variant	Exon 6 of 6	5	NM_198285.3	ENSP00000335522.7		Q86TI4-3

Frequencies

GnomAD3 genomes

Cov.:

GnomAD4 exome

Data not reliable, filtered out with message: AC0

AF:

0.00

AC:

AN:

1337026

Hom.:

Cov.:

AF XY:

0.00

AC XY:

AN XY:

657988

African (AFR)

AF:

0.00

AC:

AN:

26790

American (AMR)

AF:

0.00

AC:

AN:

25006

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

21640

East Asian (EAS)

AF:

0.00

AC:

AN:

32798

South Asian (SAS)

AF:

0.00

AC:

AN:

70934

European-Finnish (FIN)

AF:

0.00

AC:

AN:

42014

Middle Eastern (MID)

AF:

0.00

AC:

AN:

4070

European-Non Finnish (NFE)

AF:

0.00

AC:

AN:

1058618

Other (OTH)

AF:

0.00

AC:

AN:

55156

GnomAD4 genome

Cov.:

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Pathogenic

0.76

BayesDel_addAF

Uncertain

0.086

BayesDel_noAF

Benign

-0.19

CADD

Pathogenic

(source)

DANN

Uncertain

0.99

Eigen

Uncertain

0.43

Eigen_PC

Uncertain

0.35

FATHMM_MKL

Benign

0.38

LIST_S2

Benign

0.38

M_CAP

Pathogenic

0.78

MetaRNN

Benign

0.36

MetaSVM

Benign

-0.56

PhyloP100

0.57

PROVEAN

Benign

-0.24

REVEL

Benign

0.16

Sift

Pathogenic

0.0

Sift4G

Benign

0.52

Vest4

0.17

MutPred

0.33

Gain of catalytic residue at A359 (P = 0.0061);

MVP

0.57

ClinPred

0.99

GERP RS

3.5

Varity_R

0.60

gMVP

0.10

Mutation Taster

=55/45

polymorphism

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

Other links and lift over