NM_001367482.1:c.2596-280A>C

Variant names:

• chr1-241782992-A-C
• rs952084
• NM_001367482.1:c.2596-280A>C

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_001367482.1(WDR64):​c.2596-280A>C variant causes a intron 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.

• Frequency: Genomes: not found (cov: 33)
• Consequence: WDR64 NM_001367482.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.350
• Publications: 2 publications found

Genes affected

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

ENSG00000288723 (HGNC:):

ACMG classification

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

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001367482.1. 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
	WDR64	NM_001367482.1	MANE Select	c.2596-280A>C		intron	N/A	NP_001354411.1	A0A0C4DG52

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	WDR64	ENST00000437684.7	TSL:1 MANE Select	c.2596-280A>C		intron	N/A	ENSP00000402446.4	A0A0C4DG52
	WDR64	ENST00000366552.6	TSL:5	c.2566-280A>C		intron	N/A	ENSP00000355510.2	B1ANS9-1
	WDR64	ENST00000414635.5	TSL:5	c.1378-280A>C		intron	N/A	ENSP00000406656.1	A0A0A0MSY1

Frequencies

GnomAD3 genomes Cov.: 33

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome Cov.: 33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	4.8
DANN	Benign	0.46
PhyloP100		0.35

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: rs952084; hg19: chr1-241946294;