chr1-241722005-C-T

Variant names:

• chr1-241722005-C-T
• rs7519667
• NM_001367482.1:c.1055-1292C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001367482.1(WDR64):​c.1055-1292C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.773 in 151,960 control chromosomes in the GnomAD database, including 45,749 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 0.77 (45749 hom., cov: 31)
• Consequence: WDR64 NM_001367482.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0360
• Publications: 1 publications found

Genes affected

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

LOC124904603 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.816 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001367482.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	WDR64	NM_001367482.1	MANE Select	c.1055-1292C>T		intron	N/A	NP_001354411.1	A0A0C4DG52

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	WDR64	ENST00000437684.7	TSL:1 MANE Select	c.1055-1292C>T		intron	N/A	ENSP00000402446.4	A0A0C4DG52
	WDR64	ENST00000366552.6	TSL:5	c.1025-1292C>T		intron	N/A	ENSP00000355510.2	B1ANS9-1
	WDR64	ENST00000414635.5	TSL:5	c.338-1292C>T		intron	N/A	ENSP00000406656.1	A0A0A0MSY1

Frequencies

GnomAD3 genomes AF: 0.773 AC: 117410 AN: 151842 Hom.: 45707 Cov.: 31

Gnomad AFR AF: 0.759

Gnomad AMI AF: 0.795

Gnomad AMR AF: 0.738

Gnomad ASJ AF: 0.836

Gnomad EAS AF: 0.491

Gnomad SAS AF: 0.708

Gnomad FIN AF: 0.712

Gnomad MID AF: 0.788

Gnomad NFE AF: 0.822

Gnomad OTH AF: 0.770

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

GnomAD4 genome AF: 0.773 AC: 117503 AN: 151960 Hom.: 45749 Cov.: 31 AF XY: 0.765 AC XY: 56807 AN XY: 74260

African (AFR) AF: 0.759 AC: 31479 AN: 41472

American (AMR) AF: 0.737 AC: 11231 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.836 AC: 2900 AN: 3468

East Asian (EAS) AF: 0.491 AC: 2531 AN: 5150

South Asian (SAS) AF: 0.709 AC: 3419 AN: 4822

European-Finnish (FIN) AF: 0.712 AC: 7494 AN: 10532

Middle Eastern (MID) AF: 0.803 AC: 236 AN: 294

European-Non Finnish (NFE) AF: 0.822 AC: 55863 AN: 67952

Other (OTH) AF: 0.770 AC: 1627 AN: 2112

Alfa AF: 0.804 Hom.: 199104

Bravo AF: 0.775

Asia WGS AF: 0.637 AC: 2218 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	3.1
DANN	Benign	0.39
PhyloP100		0.036
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: rs7519667; hg19: chr1-241885307;