1-241782615-C-T

Position:

• chr1-241782615-C-T

Variant summary

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

The NM_001367482.1(WDR64):​c.2596-657C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0891 in 152,136 control chromosomes in the GnomAD database, including 799 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 0.089 (799 hom., cov: 32)
• Consequence: WDR64 NM_001367482.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.429

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=-0.85).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.147 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
WDR64	NM_001367482.1	c.2596-657C>T		intron_variant		ENST00000437684.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
WDR64	ENST00000437684.7	c.2596-657C>T		intron_variant		1	NM_001367482.1	P1
	ENST00000684005.1	n.161-17431G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.0891 AC: 13539 AN: 152020 Hom.: 789 Cov.: 32

Gnomad AFR AF: 0.0219

Gnomad AMI AF: 0.0844

Gnomad AMR AF: 0.152

Gnomad ASJ AF: 0.0614

Gnomad EAS AF: 0.144

Gnomad SAS AF: 0.137

Gnomad FIN AF: 0.129

Gnomad MID AF: 0.0443

Gnomad NFE AF: 0.104

Gnomad OTH AF: 0.0872

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

GnomAD4 genome AF: 0.0891 AC: 13555 AN: 152136 Hom.: 799 Cov.: 32 AF XY: 0.0911 AC XY: 6776 AN XY: 74364

Gnomad4 AFR AF: 0.0218

Gnomad4 AMR AF: 0.152

Gnomad4 ASJ AF: 0.0614

Gnomad4 EAS AF: 0.144

Gnomad4 SAS AF: 0.137

Gnomad4 FIN AF: 0.129

Gnomad4 NFE AF: 0.104

Gnomad4 OTH AF: 0.0958

Alfa AF: 0.103 Hom.: 1183

Bravo AF: 0.0900

Asia WGS AF: 0.181 AC: 627 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	2.7
DANN	Benign	0.80

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: rs4658506; hg19: chr1-241945917;