rs6429302

chr1-241750006-T-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001367482.1(WDR64):c.1770+284T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.15 in 152,218 control chromosomes in the GnomAD database, including 1,900 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 0.15 (1900 hom., cov: 32)
• Consequence: WDR64 NM_001367482.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.805

Genes affected

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

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.182 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
WDR64	NM_001367482.1	c.1770+284T>G		intron_variant		ENST00000437684.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
WDR64	ENST00000437684.7	c.1770+284T>G		intron_variant		1	NM_001367482.1	P1
	ENST00000684005.1	n.284-7900A>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.150 AC: 22752 AN: 152100 Hom.: 1901 Cov.: 32

Gnomad AFR AF: 0.186

Gnomad AMI AF: 0.163

Gnomad AMR AF: 0.123

Gnomad ASJ AF: 0.197

Gnomad EAS AF: 0.00135

Gnomad SAS AF: 0.0284

Gnomad FIN AF: 0.0843

Gnomad MID AF: 0.0538

Gnomad NFE AF: 0.162

Gnomad OTH AF: 0.134

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

GnomAD4 genome AF: 0.150 AC: 22768 AN: 152218 Hom.: 1900 Cov.: 32 AF XY: 0.143 AC XY: 10669 AN XY: 74440

Gnomad4 AFR AF: 0.186

Gnomad4 AMR AF: 0.123

Gnomad4 ASJ AF: 0.197

Gnomad4 EAS AF: 0.00135

Gnomad4 SAS AF: 0.0284

Gnomad4 FIN AF: 0.0843

Gnomad4 NFE AF: 0.162

Gnomad4 OTH AF: 0.133

Alfa AF: 0.148 Hom.: 788

Bravo AF: 0.154

Asia WGS AF: 0.0370 AC: 129 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
Cadd	Benign	6.5
Dann	Benign	0.61

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

Publications

LitVar

Other links and lift over

dbSNP: rs6429302; hg19: chr1-241913308;