NM_001367482.1:c.2596-657C>T

Variant names:

• chr1-241782615-C-T
• rs4658506
• NM_001367482.1:c.2596-657C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001367482.1(WDR64):​c.2596-657C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0891 in 152,136 control chromosomes in the GnomAD database, including 799 homozygotes. 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: 𝑓 0.089 (799 hom., cov: 32)
• Consequence: WDR64 NM_001367482.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.429
• Publications: 1 publications found

Genes affected

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

ENSG00000288723 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.147 is higher than 0.05.

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.2596-657C>T		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.2596-657C>T		intron	N/A	ENSP00000402446.4	A0A0C4DG52
	WDR64	ENST00000366552.6	TSL:5	c.2566-657C>T		intron	N/A	ENSP00000355510.2	B1ANS9-1
	WDR64	ENST00000414635.5	TSL:5	c.1378-657C>T		intron	N/A	ENSP00000406656.1	A0A0A0MSY1

Frequencies

GnomAD3 genomes AF: 0.0891 AC: 13539 AN: 152020 Hom.: 789 Cov.: 32

Gnomad AFR AF: 0.0219

Gnomad AMI AF: 0.0844

Gnomad AMR AF: 0.152

Gnomad ASJ AF: 0.0614

Gnomad EAS AF: 0.144

Gnomad SAS AF: 0.137

Gnomad FIN AF: 0.129

Gnomad MID AF: 0.0443

Gnomad NFE AF: 0.104

Gnomad OTH AF: 0.0872

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

GnomAD4 genome AF: 0.0891 AC: 13555 AN: 152136 Hom.: 799 Cov.: 32 AF XY: 0.0911 AC XY: 6776 AN XY: 74364

African (AFR) AF: 0.0218 AC: 907 AN: 41542

American (AMR) AF: 0.152 AC: 2320 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.0614 AC: 213 AN: 3468

East Asian (EAS) AF: 0.144 AC: 739 AN: 5140

South Asian (SAS) AF: 0.137 AC: 659 AN: 4812

European-Finnish (FIN) AF: 0.129 AC: 1360 AN: 10576

Middle Eastern (MID) AF: 0.0476 AC: 14 AN: 294

European-Non Finnish (NFE) AF: 0.104 AC: 7064 AN: 68008

Other (OTH) AF: 0.0958 AC: 202 AN: 2108

Alfa AF: 0.102 Hom.: 1628

Bravo AF: 0.0900

Asia WGS AF: 0.181 AC: 627 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	2.7
DANN	Benign	0.80
PhyloP100		-0.43
Mutation Taster		=100/0	polymorphism (auto)

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: rs4658506; hg19: chr1-241945917;