rs1342866

Variant names:

• chr1-241797367-C-T
• rs1342866
• NM_001367482.1:c.3192+997C>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.3192+997C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.785 in 152,096 control chromosomes in the GnomAD database, including 48,283 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 0.79 (48283 hom., cov: 32)
• Consequence: WDR64 NM_001367482.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.171
• 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=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.975 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
WDR64	NM_001367482.1	c.3192+997C>T		intron_variant	Intron 27 of 27	ENST00000437684.7	NP_001354411.1
WDR64	XM_017000315.2	c.2940+997C>T		intron_variant	Intron 27 of 27		XP_016855804.1
WDR64	XM_011544086.4	c.2709+997C>T		intron_variant	Intron 25 of 25		XP_011542388.1
WDR64	XM_047445900.1	c.2709+997C>T		intron_variant	Intron 24 of 24		XP_047301856.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
WDR64	ENST00000437684.7	c.3192+997C>T		intron_variant	Intron 27 of 27	1	NM_001367482.1	ENSP00000402446.4

Frequencies

GnomAD3 genomes AF: 0.785 AC: 119374 AN: 151978 Hom.: 48252 Cov.: 32

Gnomad AFR AF: 0.584

Gnomad AMI AF: 0.767

Gnomad AMR AF: 0.857

Gnomad ASJ AF: 0.804

Gnomad EAS AF: 0.997

Gnomad SAS AF: 0.968

Gnomad FIN AF: 0.916

Gnomad MID AF: 0.940

Gnomad NFE AF: 0.840

Gnomad OTH AF: 0.828

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

GnomAD4 genome AF: 0.785 AC: 119460 AN: 152096 Hom.: 48283 Cov.: 32 AF XY: 0.794 AC XY: 59039 AN XY: 74374

African (AFR) AF: 0.584 AC: 24199 AN: 41432

American (AMR) AF: 0.858 AC: 13098 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.804 AC: 2793 AN: 3472

East Asian (EAS) AF: 0.997 AC: 5167 AN: 5180

South Asian (SAS) AF: 0.968 AC: 4675 AN: 4832

European-Finnish (FIN) AF: 0.916 AC: 9702 AN: 10594

Middle Eastern (MID) AF: 0.939 AC: 276 AN: 294

European-Non Finnish (NFE) AF: 0.840 AC: 57098 AN: 67994

Other (OTH) AF: 0.830 AC: 1754 AN: 2114

Alfa AF: 0.819 Hom.: 139736

Bravo AF: 0.772

Asia WGS AF: 0.945 AC: 3286 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.72
DANN	Benign	0.23
PhyloP100		-0.17
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: rs1342866; hg19: chr1-241960669;