1-241728933-T-C

Position:

• chr1-241728933-T-C

Variant summary

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

The NM_001367482.1(WDR64):​c.1194+5497T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.193 in 152,030 control chromosomes in the GnomAD database, including 3,463 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 0.19 (3463 hom., cov: 32)
• Consequence: WDR64 NM_001367482.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.745

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=-0.8).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.323 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
WDR64	NM_001367482.1	c.1194+5497T>C		intron_variant		ENST00000437684.7
LOC124904603	XR_007067055.1	n.189+13126A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
WDR64	ENST00000437684.7	c.1194+5497T>C		intron_variant		1	NM_001367482.1	P1
	ENST00000684005.1	n.332-99A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.193 AC: 29278 AN: 151912 Hom.: 3456 Cov.: 32

Gnomad AFR AF: 0.328

Gnomad AMI AF: 0.146

Gnomad AMR AF: 0.159

Gnomad ASJ AF: 0.170

Gnomad EAS AF: 0.197

Gnomad SAS AF: 0.128

Gnomad FIN AF: 0.0848

Gnomad MID AF: 0.185

Gnomad NFE AF: 0.141

Gnomad OTH AF: 0.179

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

GnomAD4 genome AF: 0.193 AC: 29315 AN: 152030 Hom.: 3463 Cov.: 32 AF XY: 0.190 AC XY: 14086 AN XY: 74324

Gnomad4 AFR AF: 0.328

Gnomad4 AMR AF: 0.159

Gnomad4 ASJ AF: 0.170

Gnomad4 EAS AF: 0.198

Gnomad4 SAS AF: 0.129

Gnomad4 FIN AF: 0.0848

Gnomad4 NFE AF: 0.141

Gnomad4 OTH AF: 0.177

Alfa AF: 0.148 Hom.: 2045

Bravo AF: 0.206

Asia WGS AF: 0.165 AC: 570 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	9.0
DANN	Benign	0.85

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: rs9782914; hg19: chr1-241892235;