1-241652598-T-G

Position:

• chr1-241652598-T-G

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_001367482.1(WDR64):​c.114T>G​(p.Asp38Glu) 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. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

• Frequency: Genomes: not found (cov: 33)
• Consequence: WDR64 NM_001367482.1 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.529

Genes affected

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

OPN3 (HGNC:14007): (opsin 3) Opsins are members of the guanine nucleotide-binding protein (G protein)-coupled receptor superfamily. In addition to the visual opsins, mammals possess several photoreceptive non-visual opsins that are expressed in extraocular tissues. This gene, opsin 3, is strongly expressed in brain and testis and weakly expressed in liver, placenta, heart, lung, skeletal muscle, kidney, and pancreas. The gene may also be expressed in the retina. The protein has the canonical features of a photoreceptive opsin protein. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Likely_benign. Variant got -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.046492487).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
WDR64	NM_001367482.1	c.114T>G	p.Asp38Glu	missense_variant	1/28	ENST00000437684.7
WDR64	XM_011544087.3	c.114T>G	p.Asp38Glu	missense_variant	1/23
WDR64	XM_011544091.2	c.114T>G	p.Asp38Glu	missense_variant	1/20
WDR64	XM_011544092.3	c.114T>G	p.Asp38Glu	missense_variant	1/19

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
WDR64	ENST00000437684.7	c.114T>G	p.Asp38Glu	missense_variant	1/28	1	NM_001367482.1	P1
WDR64	ENST00000366552.6	c.114T>G	p.Asp38Glu	missense_variant	1/27	5
WDR64	ENST00000425826.3	c.114T>G	p.Asp38Glu	missense_variant, NMD_transcript_variant	1/29	2
OPN3	ENST00000463155.5	n.74+24705A>C		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Cov.: 31

GnomAD4 genome Cov.: 33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.12
BayesDel_addAF	Benign	-0.37	T
BayesDel_noAF	Benign	-0.77
CADD	Benign	3.9
DANN	Uncertain	0.99
DEOGEN2	Benign	0.00073	T
Eigen	Benign	-0.65
Eigen_PC	Benign	-0.66
FATHMM_MKL	Benign	0.20	N
LIST_S2	Benign	0.50	T
M_CAP	Benign	0.0042	T
MetaRNN	Benign	0.046	T
MetaSVM	Benign	-0.97	T
MutationAssessor	Benign	0.90	L
MutationTaster	Benign	0.99	N;N
PrimateAI	Benign	0.34	T
PROVEAN	Benign	0.44	N
REVEL	Benign	0.13
Sift	Benign	0.69	T
Sift4G	Benign	0.89	T
Vest4		0.041
MutPred		0.18		Gain of loop (P = 0.1069);
MVP		0.040
MPC		0.069
ClinPred		0.10	T
GERP RS		-6.2
Varity_R		0.041
gMVP		0.054

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.020		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: chr1-241815900;