Variant 15-53716598-T-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_182758.4(WDR72):c.339+9A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.753 in 1,567,246 control chromosomes in the GnomAD database, including 446,002 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.74 ( 41806 hom., cov: 33)

Exomes 𝑓: 0.75 ( 404196 hom. )

Consequence

WDR72
NM_182758.4 intron

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:5

Conservation

PhyloP100: -1.45

Variant links:

Genes affected

WDR72 (HGNC:26790): (WD repeat domain 72) This gene encodes a protein with eight WD-40 repeats. Mutations in this gene have been associated with amelogenesis imperfecta hypomaturation type 2A3. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Mar 2013]

WDR72 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.85).

BP6

Variant 15-53716598-T-C is Benign according to our data. Variant chr15-53716598-T-C is described in ClinVar as [Benign]. Clinvar id is 263002.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr15-53716598-T-C is described in Lovd as [Benign].

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.776 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
WDR72	NM_182758.4 linkuse as main transcript	c.339+9A>G		intron_variant		ENST00000360509.10	NP_877435.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
WDR72	ENST00000360509.10 linkuse as main transcript	c.339+9A>G		intron_variant		1	NM_182758.4	ENSP00000353699	P4

Frequencies

GnomAD3 genomes

AF:

0.741

AC:

112577

AN:

151994

Hom.:

41787

Cov.:

show subpopulations

Gnomad AFR

AF:

0.729

Gnomad AMI

AF:

0.816

Gnomad AMR

AF:

0.734

Gnomad ASJ

AF:

0.784

Gnomad EAS

AF:

0.730

Gnomad SAS

AF:

0.796

Gnomad FIN

AF:

0.647

Gnomad MID

AF:

0.801

Gnomad NFE

AF:

0.757

Gnomad OTH

AF:

0.740

GnomAD3 exomes

AF:

0.745

AC:

187005

AN:

251122

Hom.:

69813

AF XY:

0.748

AC XY:

101469

AN XY:

135702

show subpopulations

Gnomad AFR exome

AF:

0.729

Gnomad AMR exome

AF:

0.720

Gnomad ASJ exome

AF:

0.771

Gnomad EAS exome

AF:

0.740

Gnomad SAS exome

AF:

0.800

Gnomad FIN exome

AF:

0.661

Gnomad NFE exome

AF:

0.754

Gnomad OTH exome

AF:

0.746

GnomAD4 exome

AF:

0.755

AC:

1067939

AN:

1415134

Hom.:

404196

Cov.:

AF XY:

0.756

AC XY:

534555

AN XY:

706786

show subpopulations

Gnomad4 AFR exome

AF:

0.728

Gnomad4 AMR exome

AF:

0.723

Gnomad4 ASJ exome

AF:

0.764

Gnomad4 EAS exome

AF:

0.741

Gnomad4 SAS exome

AF:

0.797

Gnomad4 FIN exome

AF:

0.668

Gnomad4 NFE exome

AF:

0.758

Gnomad4 OTH exome

AF:

0.759

GnomAD4 genome

AF:

0.741

AC:

112648

AN:

152112

Hom.:

41806

Cov.:

AF XY:

0.737

AC XY:

54790

AN XY:

74358

show subpopulations

Gnomad4 AFR

AF:

0.729

Gnomad4 AMR

AF:

0.734

Gnomad4 ASJ

AF:

0.784

Gnomad4 EAS

AF:

0.730

Gnomad4 SAS

AF:

0.797

Gnomad4 FIN

AF:

0.647

Gnomad4 NFE

AF:

0.757

Gnomad4 OTH

AF:

0.745

Alfa

AF:

0.756

Hom.:

101084

Bravo

AF:

0.745

Asia WGS

AF:

0.751

AC:

2609

AN:

3476

EpiCase

AF:

0.761

EpiControl

AF:

0.763

ClinVar

Significance: Benign

Submissions summary: Benign:5

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	Nov 12, 2018	- -

Amelogenesis imperfecta hypomaturation type 2A3

Benign:1

Benign, criteria provided, single submitter

clinical testing

Genome-Nilou Lab

Dec 05, 2021

- -

not specified

Benign:1

Benign, criteria provided, single submitter

clinical testing

PreventionGenetics, part of Exact Sciences

- -

Amelogenesis Imperfecta, Recessive

Benign:1

Benign, criteria provided, single submitter

clinical testing

Illumina Laboratory Services, Illumina

Jun 14, 2016

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.85

CADD

Benign

0.038

DANN

Benign

0.61

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.010

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over