7-151381734-C-A

Variant names:

• chr7-151381734-C-A
• rs1210963311
• NM_198285.3:c.979G>T

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 0P and 2B. BP4_Moderate

The NM_198285.3(WDR86):​c.979G>T​(p.Val327Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000513 in 1,363,788 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/19 in silico tools predict 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. V327M) has been classified as Uncertain significance.

• Frequency:
  • Genomes: not found (cov: 34)
  • Exomes 𝑓: 0.0000051 (0 hom.)
• Consequence: WDR86 NM_198285.3 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.430
• Publications: 0 publications found

Genes affected

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

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• BP4: Computational evidence support a benign effect (MetaRNN=0.19106352).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_198285.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	WDR86	NM_198285.3	MANE Select	c.979G>T	p.Val327Leu	missense	Exon 6 of 6	NP_938026.2	Q86TI4-3
	WDR86	NM_001284260.2		c.1043G>T	p.Gly348Val	missense	Exon 6 of 6	NP_001271189.1	Q86TI4-4
	WDR86	NM_001284261.2		c.459G>T	p.Arg153Ser	missense	Exon 5 of 5	NP_001271190.1	Q86TI4-2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	WDR86	ENST00000334493.11	TSL:5 MANE Select	c.979G>T	p.Val327Leu	missense	Exon 6 of 6	ENSP00000335522.7	Q86TI4-3
	WDR86	ENST00000469830.2	TSL:2	c.1043G>T	p.Gly348Val	missense	Exon 6 of 6	ENSP00000419162.2	Q86TI4-4
	WDR86	ENST00000477459.5	TSL:2	c.459G>T	p.Arg153Ser	missense	Exon 5 of 5	ENSP00000417512.1	Q86TI4-2

Frequencies

GnomAD3 genomes Cov.: 34

GnomAD4 exome AF: 0.00000513 AC: 7 AN: 1363788 Hom.: 0 Cov.: 54 AF XY: 0.00000745 AC XY: 5 AN XY: 671072

African (AFR) AF: 0.00 AC: 0 AN: 29664

American (AMR) AF: 0.000234 AC: 7 AN: 29972

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 22712

East Asian (EAS) AF: 0.00 AC: 0 AN: 35022

South Asian (SAS) AF: 0.00 AC: 0 AN: 74422

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 45546

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 4758

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 1065456

Other (OTH) AF: 0.00 AC: 0 AN: 56236

GnomAD4 genome Cov.: 34

Alfa AF: 0.00 Hom.: 0

Bravo AF: 0.00000378

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.15
BayesDel_addAF	Uncertain	0.091	D
BayesDel_noAF	Benign	-0.27
CADD	Benign	18
DANN	Uncertain	0.99
Eigen	Benign	-0.63
Eigen_PC	Benign	-0.37
FATHMM_MKL	Benign	0.15	N
LIST_S2	Benign	0.39	T
M_CAP	Pathogenic	0.57	D
MetaRNN	Benign	0.19	T
MetaSVM	Benign	-1.0	T
PhyloP100		0.43
PROVEAN	Benign	-2.0	N
REVEL	Benign	0.14
Sift	Pathogenic	0.0	D
Sift4G	Benign	0.12	T
Vest4		0.21
MutPred		0.39		Loss of loop (P = 0.0288)
MVP		0.57
ClinPred		0.89	D
GERP RS		3.6
Varity_R		0.12
gMVP		0.45
Mutation Taster		=88/12	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

Other links and lift over

dbSNP: rs1210963311; hg19: chr7-151078820;