rs7180849

Variant names:

• chr15-84652428-T-C
• rs7180849
• NM_032856.5:c.198+286A>G

Your query was ambiguous. Multiple possible variants found:

• chr15-84652428-T-C
• chr15-84652428-T-A
• chr15-84652428-T-G

Variant summary

Our verdict is Benign. The variant received -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The NM_032856.5(WDR73):​c.198+286A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.872 in 152,150 control chromosomes in the GnomAD database, including 58,089 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.87 (58089 hom., cov: 31)
• Consequence: WDR73 NM_032856.5 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.155
• Publications: 6 publications found

Genes affected

WDR73 (HGNC:25928): (WD repeat domain 73) The protein encoded by this gene is thought to contain multiple WD40 repeats. WD40 repeats are motifs that contain 40-60 amino acids, and usually end with Trp-Asp (WD). This protein is found in the cytoplasm during interphase, but accumulates at the spindle poles and astral microtubules during mitosis. Reduced expression of this gene results in abnormalities in the size and morphology of the nucleus. Mutations in this gene have been associated with Galloway-Mowat syndrome PMID: 25466283), which is a rare autosomal recessive disorder that affects both the central nervous system and kidneys. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Feb 2015]

WDR73 Gene-Disease associations (from GenCC):

• Galloway-Mowat syndrome 1

  Inheritance: AR Classification: STRONG Submitted by: Labcorp Genetics (formerly Invitae)
• CAMOS syndrome

  Inheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet
• Galloway-Mowat syndrome

  Inheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet

ENSG00000291159 (HGNC:58684):

ACMG classification

Our verdict: Benign. The variant received -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BP6: Variant 15-84652428-T-C is Benign according to our data. Variant chr15-84652428-T-C is described in ClinVar as Benign. ClinVar VariationId is 1258449.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.943 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_032856.5. 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
	WDR73	NM_032856.5	MANE Select	c.198+286A>G		intron	N/A	NP_116245.2	Q6P4I2
	WDR73	NR_130944.2		n.741+286A>G		intron	N/A
	WDR73	NR_130945.2		n.207+286A>G		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	WDR73	ENST00000434634.7	TSL:1 MANE Select	c.198+286A>G		intron	N/A	ENSP00000387982.3	Q6P4I2
	WDR73	ENST00000398528.7	TSL:1	n.274+286A>G		intron	N/A
	WDR73	ENST00000948303.1		c.195+286A>G		intron	N/A	ENSP00000618362.1

Frequencies

GnomAD3 genomes AF: 0.872 AC: 132567 AN: 152032 Hom.: 58026 Cov.: 31

Gnomad AFR AF: 0.951

Gnomad AMI AF: 0.843

Gnomad AMR AF: 0.883

Gnomad ASJ AF: 0.881

Gnomad EAS AF: 0.944

Gnomad SAS AF: 0.803

Gnomad FIN AF: 0.795

Gnomad MID AF: 0.861

Gnomad NFE AF: 0.833

Gnomad OTH AF: 0.862

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

GnomAD4 genome AF: 0.872 AC: 132686 AN: 152150 Hom.: 58089 Cov.: 31 AF XY: 0.870 AC XY: 64680 AN XY: 74354

African (AFR) AF: 0.951 AC: 39467 AN: 41516

American (AMR) AF: 0.883 AC: 13510 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.881 AC: 3056 AN: 3470

East Asian (EAS) AF: 0.944 AC: 4891 AN: 5182

South Asian (SAS) AF: 0.804 AC: 3866 AN: 4808

European-Finnish (FIN) AF: 0.795 AC: 8402 AN: 10566

Middle Eastern (MID) AF: 0.867 AC: 255 AN: 294

European-Non Finnish (NFE) AF: 0.833 AC: 56662 AN: 67998

Other (OTH) AF: 0.857 AC: 1808 AN: 2110

Alfa AF: 0.856 Hom.: 12671

Bravo AF: 0.883

Asia WGS AF: 0.881 AC: 3063 AN: 3478

ClinVar

ClinVar submissions

Significance: Benign

Revision: criteria provided, single submitter

Pathogenic	VUS	Benign	Condition
-	-	1	not provided (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	2.0
DANN	Benign	0.29
PhyloP100		-0.15
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: rs7180849; hg19: chr15-85195659;