1-241652507-G-C

Position:

• chr1-241652507-G-C

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2 BP4_Moderate

The NM_001367482.1(WDR64):​c.23G>C​(p.Arg8Pro) 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. 15/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R8C) has been classified as Uncertain significance.

• Frequency: Genomes: not found (cov: 33)
• Consequence: WDR64 NM_001367482.1 missense
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1
• Conservation: PhyloP100: -2.47

Genes affected

WDR64 (HGNC:26570): (WD repeat domain 64)

OPN3 (HGNC:):

ACMG classification

Verdict is Uncertain_significance. Variant got 0 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.08117154).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
WDR64	NM_001367482.1	c.23G>C	p.Arg8Pro	missense_variant	1/28	ENST00000437684.7	NP_001354411.1
WDR64	XM_011544087.3	c.23G>C	p.Arg8Pro	missense_variant	1/23		XP_011542389.1
WDR64	XM_011544091.2	c.23G>C	p.Arg8Pro	missense_variant	1/20		XP_011542393.1
WDR64	XM_011544092.3	c.23G>C	p.Arg8Pro	missense_variant	1/19		XP_011542394.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
WDR64	ENST00000437684.7	c.23G>C	p.Arg8Pro	missense_variant	1/28	1	NM_001367482.1	ENSP00000402446.4
WDR64	ENST00000366552.6	c.23G>C	p.Arg8Pro	missense_variant	1/27	5		ENSP00000355510.2
WDR64	ENST00000425826.3	n.23G>C		non_coding_transcript_exon_variant	1/29	2		ENSP00000406342.3
OPN3	ENST00000463155.5	n.74+24796C>G		intron_variant		3

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Cov.: 31

GnomAD4 genome Cov.: 33

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:1

Revision: criteria provided, single submitter

Submissions by phenotype

not specified Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

Ambry Genetics

Aug 12, 2021

The c.23G>C (p.R8P) alteration is located in exon 1 (coding exon 1) of the WDR64 gene. This alteration results from a G to C substitution at nucleotide position 23, causing the arginine (R) at amino acid position 8 to be replaced by a proline (P). 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	0.12
BayesDel_addAF	Benign	-0.21	T
BayesDel_noAF	Benign	-0.53
CADD	Benign	0.0020
DANN	Benign	0.58
DEOGEN2	Benign	0.0029	T
Eigen	Benign	-1.5
Eigen_PC	Benign	-1.8
FATHMM_MKL	Benign	0.050	N
LIST_S2	Benign	0.43	T
M_CAP	Benign	0.0035	T
MetaRNN	Benign	0.081	T
MetaSVM	Benign	-0.83	T
MutationAssessor	Benign	1.5	L
PrimateAI	Benign	0.25	T
PROVEAN	Benign	-0.60	N
REVEL	Benign	0.090
Sift	Benign	0.19	T
Sift4G	Benign	0.20	T
Vest4		0.17
MutPred		0.28		Loss of MoRF binding (P = 2e-04);
MVP		0.014
MPC		0.13
ClinPred		0.32	T
GERP RS		-11
Varity_R		0.098
gMVP		0.21

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.

Other links and lift over

hg19: chr1-241815809;