rs953597

Variant names:

• chr1-241783464-A-C
• rs953597
• NM_001367482.1:c.2705+83A>C

Your query was ambiguous. Multiple possible variants found:

• chr1-241783464-A-C
• chr1-241783464-A-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.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
• Publications: 5 publications found

Genes affected

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

ENSG00000288723 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

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.2705+83A>C		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.2705+83A>C		intron	N/A	ENSP00000402446.4	A0A0C4DG52
	WDR64	ENST00000366552.6	TSL:5	c.2675+83A>C		intron	N/A	ENSP00000355510.2	B1ANS9-1
	WDR64	ENST00000414635.5	TSL:5	c.1487+83A>C		intron	N/A	ENSP00000406656.1	A0A0A0MSY1

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

African (AFR) AF: 0.485 AC: 9361 AN: 19314

American (AMR) AF: 0.467 AC: 10889 AN: 23314

Ashkenazi Jewish (ASJ) AF: 0.760 AC: 14344 AN: 18886

East Asian (EAS) AF: 0.412 AC: 14107 AN: 34280

South Asian (SAS) AF: 0.527 AC: 32123 AN: 61008

European-Finnish (FIN) AF: 0.578 AC: 25446 AN: 43998

Middle Eastern (MID) AF: 0.616 AC: 2744 AN: 4458

European-Non Finnish (NFE) AF: 0.695 AC: 423153 AN: 608750

Other (OTH) AF: 0.641 AC: 25302 AN: 39446

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

African (AFR) AF: 0.494 AC: 20467 AN: 41460

American (AMR) AF: 0.535 AC: 8171 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.755 AC: 2621 AN: 3472

East Asian (EAS) AF: 0.434 AC: 2246 AN: 5174

South Asian (SAS) AF: 0.507 AC: 2441 AN: 4812

European-Finnish (FIN) AF: 0.575 AC: 6079 AN: 10572

Middle Eastern (MID) AF: 0.697 AC: 205 AN: 294

European-Non Finnish (NFE) AF: 0.697 AC: 47331 AN: 67922

Other (OTH) AF: 0.590 AC: 1244 AN: 2110

Alfa AF: 0.660 Hom.: 73310

Bravo AF: 0.591

Asia WGS AF: 0.449 AC: 1566 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.4
DANN	Benign	0.51
PhyloP100		-0.0030
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: rs953597; hg19: chr1-241946766;