1-241728933-T-C

Variant names:

• chr1-241728933-T-C
• rs9782914
• NM_001367482.1:c.1194+5497T>C

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+5497T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.193 in 152,030 control chromosomes in the GnomAD database, including 3,463 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 0.19 (3463 hom., cov: 32)
• Consequence: WDR64 NM_001367482.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.745
• Publications: 3 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=-0.8).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.323 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
WDR64	NM_001367482.1	c.1194+5497T>C		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+5497T>C		intron_variant	Intron 10 of 27	1	NM_001367482.1	ENSP00000402446.4

Frequencies

GnomAD3 genomes AF: 0.193 AC: 29278 AN: 151912 Hom.: 3456 Cov.: 32

Gnomad AFR AF: 0.328

Gnomad AMI AF: 0.146

Gnomad AMR AF: 0.159

Gnomad ASJ AF: 0.170

Gnomad EAS AF: 0.197

Gnomad SAS AF: 0.128

Gnomad FIN AF: 0.0848

Gnomad MID AF: 0.185

Gnomad NFE AF: 0.141

Gnomad OTH AF: 0.179

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

GnomAD4 genome AF: 0.193 AC: 29315 AN: 152030 Hom.: 3463 Cov.: 32 AF XY: 0.190 AC XY: 14086 AN XY: 74324

African (AFR) AF: 0.328 AC: 13585 AN: 41422

American (AMR) AF: 0.159 AC: 2429 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.170 AC: 590 AN: 3468

East Asian (EAS) AF: 0.198 AC: 1025 AN: 5182

South Asian (SAS) AF: 0.129 AC: 619 AN: 4814

European-Finnish (FIN) AF: 0.0848 AC: 897 AN: 10576

Middle Eastern (MID) AF: 0.178 AC: 52 AN: 292

European-Non Finnish (NFE) AF: 0.141 AC: 9611 AN: 67994

Other (OTH) AF: 0.177 AC: 374 AN: 2108

Alfa AF: 0.153 Hom.: 2976

Bravo AF: 0.206

Asia WGS AF: 0.165 AC: 570 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	9.0
DANN	Benign	0.85
PhyloP100		0.74
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: rs9782914; hg19: chr1-241892235;