chr1-241715245-T-G

Position:

• chr1-241715245-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.1054+3364T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.156 in 152,216 control chromosomes in the GnomAD database, including 2,236 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 0.16 (2236 hom., cov: 32)
• Consequence: WDR64 NM_001367482.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.40

Genes affected

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

LOC124904603 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.207 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
WDR64	NM_001367482.1	c.1054+3364T>G		intron_variant		ENST00000437684.7
LOC124904603	XR_007067055.1	n.189+26814A>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
WDR64	ENST00000437684.7	c.1054+3364T>G		intron_variant		1	NM_001367482.1	P1
WDR64	ENST00000366552.6	c.1024+3364T>G		intron_variant		5
WDR64	ENST00000414635.5	c.337+3364T>G		intron_variant		5
WDR64	ENST00000425826.3	c.1054+3364T>G		intron_variant, NMD_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.156 AC: 23767 AN: 152098 Hom.: 2235 Cov.: 32

Gnomad AFR AF: 0.0631

Gnomad AMI AF: 0.220

Gnomad AMR AF: 0.147

Gnomad ASJ AF: 0.256

Gnomad EAS AF: 0.0839

Gnomad SAS AF: 0.195

Gnomad FIN AF: 0.163

Gnomad MID AF: 0.328

Gnomad NFE AF: 0.210

Gnomad OTH AF: 0.169

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

GnomAD4 genome AF: 0.156 AC: 23762 AN: 152216 Hom.: 2236 Cov.: 32 AF XY: 0.154 AC XY: 11460 AN XY: 74428

Gnomad4 AFR AF: 0.0629

Gnomad4 AMR AF: 0.147

Gnomad4 ASJ AF: 0.256

Gnomad4 EAS AF: 0.0845

Gnomad4 SAS AF: 0.196

Gnomad4 FIN AF: 0.163

Gnomad4 NFE AF: 0.210

Gnomad4 OTH AF: 0.166

Alfa AF: 0.198 Hom.: 4687

Bravo AF: 0.150

Asia WGS AF: 0.122 AC: 425 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	7.6
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: rs12569163; hg19: chr1-241878547;