chr1-241730784-C-A

Variant names:

• chr1-241730784-C-A
• rs10926554
• NM_001367482.1:c.1194+7348C>A

Variant summary

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

The NM_001367482.1(WDR64):​c.1194+7348C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.157 in 152,078 control chromosomes in the GnomAD database, including 2,190 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 0.16 (2190 hom., cov: 32)
• Consequence: WDR64 NM_001367482.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.356
• Publications: 5 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=-0.73).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.272 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
WDR64	NM_001367482.1	c.1194+7348C>A		intron_variant	Intron 10 of 27	ENST00000437684.7	NP_001354411.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
WDR64	ENST00000437684.7	c.1194+7348C>A		intron_variant	Intron 10 of 27	1	NM_001367482.1	ENSP00000402446.4

Frequencies

GnomAD3 genomes AF: 0.157 AC: 23850 AN: 151960 Hom.: 2189 Cov.: 32

Gnomad AFR AF: 0.224

Gnomad AMI AF: 0.111

Gnomad AMR AF: 0.155

Gnomad ASJ AF: 0.153

Gnomad EAS AF: 0.285

Gnomad SAS AF: 0.137

Gnomad FIN AF: 0.0658

Gnomad MID AF: 0.146

Gnomad NFE AF: 0.124

Gnomad OTH AF: 0.140

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

GnomAD4 genome AF: 0.157 AC: 23865 AN: 152078 Hom.: 2190 Cov.: 32 AF XY: 0.155 AC XY: 11544 AN XY: 74328

African (AFR) AF: 0.224 AC: 9303 AN: 41466

American (AMR) AF: 0.155 AC: 2374 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.153 AC: 530 AN: 3468

East Asian (EAS) AF: 0.285 AC: 1469 AN: 5162

South Asian (SAS) AF: 0.137 AC: 661 AN: 4818

European-Finnish (FIN) AF: 0.0658 AC: 696 AN: 10584

Middle Eastern (MID) AF: 0.143 AC: 42 AN: 294

European-Non Finnish (NFE) AF: 0.124 AC: 8398 AN: 67980

Other (OTH) AF: 0.138 AC: 291 AN: 2104

Alfa AF: 0.132 Hom.: 746

Bravo AF: 0.168

Asia WGS AF: 0.187 AC: 647 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.73
CADD	Benign	15
DANN	Benign	0.77
PhyloP100		0.36
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: rs10926554; hg19: chr1-241894086;