chr1-241782992-A-G

Position:

• chr1-241782992-A-G

Variant summary

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

The NM_001367482.1(WDR64):​c.2596-280A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.211 in 152,150 control chromosomes in the GnomAD database, including 3,781 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 0.21 (3781 hom., cov: 33)
• Consequence: WDR64 NM_001367482.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.350

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=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.407 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
WDR64	NM_001367482.1	c.2596-280A>G		intron_variant		ENST00000437684.7	NP_001354411.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
WDR64	ENST00000437684.7	c.2596-280A>G		intron_variant		1	NM_001367482.1	ENSP00000402446	P1
	ENST00000684005.1	n.161-17808T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.210 AC: 32000 AN: 152032 Hom.: 3773 Cov.: 33

Gnomad AFR AF: 0.143

Gnomad AMI AF: 0.216

Gnomad AMR AF: 0.273

Gnomad ASJ AF: 0.181

Gnomad EAS AF: 0.422

Gnomad SAS AF: 0.355

Gnomad FIN AF: 0.294

Gnomad MID AF: 0.247

Gnomad NFE AF: 0.198

Gnomad OTH AF: 0.253

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

GnomAD4 genome AF: 0.211 AC: 32033 AN: 152150 Hom.: 3781 Cov.: 33 AF XY: 0.219 AC XY: 16302 AN XY: 74372

Gnomad4 AFR AF: 0.143

Gnomad4 AMR AF: 0.274

Gnomad4 ASJ AF: 0.181

Gnomad4 EAS AF: 0.422

Gnomad4 SAS AF: 0.354

Gnomad4 FIN AF: 0.294

Gnomad4 NFE AF: 0.198

Gnomad4 OTH AF: 0.252

Alfa AF: 0.208 Hom.: 6986

Bravo AF: 0.206

Asia WGS AF: 0.346 AC: 1202 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	5.3
DANN	Benign	0.42

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: rs952084; hg19: chr1-241946294;