rs953597

chr1-241783464-A-Cchr1-241783464-A-T

Variant summary

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

The NM_001367482.1(WDR64):c.2705+83A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.645 in 1,005,450 control chromosomes in the GnomAD database, including 213,844 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 0.60 (28422 hom., cov: 32)
  • Exomes 𝑓: 0.65 (185422 hom.)
• Consequence: WDR64 NM_001367482.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00300

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=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.692 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
WDR64	NM_001367482.1	c.2705+83A>C		intron_variant		ENST00000437684.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
WDR64	ENST00000437684.7	c.2705+83A>C		intron_variant		1	NM_001367482.1	P1
	ENST00000684005.1	n.161-18280T>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.602 AC: 91428 AN: 151878 Hom.: 28423 Cov.: 32

Gnomad AFR AF: 0.494

Gnomad AMI AF: 0.701

Gnomad AMR AF: 0.536

Gnomad ASJ AF: 0.755

Gnomad EAS AF: 0.434

Gnomad SAS AF: 0.506

Gnomad FIN AF: 0.575

Gnomad MID AF: 0.687

Gnomad NFE AF: 0.697

Gnomad OTH AF: 0.597

GnomAD4 exome AF: 0.653 AC: 557469 AN: 853454 Hom.: 185422 AF XY: 0.650 AC XY: 285249 AN XY: 439100

Gnomad4 AFR exome AF: 0.485

Gnomad4 AMR exome AF: 0.467

Gnomad4 ASJ exome AF: 0.760

Gnomad4 EAS exome AF: 0.412

Gnomad4 SAS exome AF: 0.527

Gnomad4 FIN exome AF: 0.578

Gnomad4 NFE exome AF: 0.695

Gnomad4 OTH exome AF: 0.641

GnomAD4 genome AF: 0.602 AC: 91443 AN: 151996 Hom.: 28422 Cov.: 32 AF XY: 0.594 AC XY: 44153 AN XY: 74300

Gnomad4 AFR AF: 0.494

Gnomad4 AMR AF: 0.535

Gnomad4 ASJ AF: 0.755

Gnomad4 EAS AF: 0.434

Gnomad4 SAS AF: 0.507

Gnomad4 FIN AF: 0.575

Gnomad4 NFE AF: 0.697

Gnomad4 OTH AF: 0.590

Alfa AF: 0.672 Hom.: 52345

Bravo AF: 0.591

Asia WGS AF: 0.449 AC: 1566 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
Cadd	Benign	1.4
Dann	Benign	0.51

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: rs953597; hg19: chr1-241946766;