Variant 15-53702296-A-G details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1

The NM_182758.4(WDR72):c.1407T>C(p.Tyr469=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.537 in 1,613,322 control chromosomes in the GnomAD database, including 237,461 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.59 ( 27141 hom., cov: 31)

Exomes 𝑓: 0.53 ( 210320 hom. )

Consequence

WDR72
NM_182758.4 synonymous

Scores

Clinical Significance

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

Conservation

PhyloP100: 1.19

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 -21 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.63).

BP6

Variant 15-53702296-A-G is Benign according to our data. Variant chr15-53702296-A-G is described in ClinVar as [Benign]. Clinvar id is 262998.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr15-53702296-A-G is described in Lovd as [Benign].

BP7

Synonymous conserved (PhyloP=1.19 with no splicing effect.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.778 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.1407T>C	p.Tyr469=	synonymous_variant	12/20	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.1407T>C	p.Tyr469=	synonymous_variant	12/20	1	NM_182758.4	ENSP00000353699	P4

Frequencies

GnomAD3 genomes

AF:

0.589

AC:

89411

AN:

151856

Hom.:

27104

Cov.:

show subpopulations

Gnomad AFR

AF:

0.684

Gnomad AMI

AF:

0.384

Gnomad AMR

AF:

0.616

Gnomad ASJ

AF:

0.394

Gnomad EAS

AF:

0.798

Gnomad SAS

AF:

0.533

Gnomad FIN

AF:

0.690

Gnomad MID

AF:

0.399

Gnomad NFE

AF:

0.512

Gnomad OTH

AF:

0.545

GnomAD3 exomes

AF:

0.583

AC:

146603

AN:

251414

Hom.:

44317

AF XY:

0.571

AC XY:

77567

AN XY:

135872

show subpopulations

Gnomad AFR exome

AF:

0.683

Gnomad AMR exome

AF:

0.698

Gnomad ASJ exome

AF:

0.406

Gnomad EAS exome

AF:

0.809

Gnomad SAS exome

AF:

0.521

Gnomad FIN exome

AF:

0.675

Gnomad NFE exome

AF:

0.514

Gnomad OTH exome

AF:

0.539

GnomAD4 exome

AF:

0.532

AC:

777548

AN:

1461348

Hom.:

210320

Cov.:

AF XY:

0.530

AC XY:

385673

AN XY:

727002

show subpopulations

Gnomad4 AFR exome

AF:

0.682

Gnomad4 AMR exome

AF:

0.689

Gnomad4 ASJ exome

AF:

0.408

Gnomad4 EAS exome

AF:

0.749

Gnomad4 SAS exome

AF:

0.528

Gnomad4 FIN exome

AF:

0.666

Gnomad4 NFE exome

AF:

0.511

Gnomad4 OTH exome

AF:

0.537

GnomAD4 genome

AF:

0.589

AC:

89510

AN:

151974

Hom.:

27141

Cov.:

AF XY:

0.597

AC XY:

44345

AN XY:

74272

show subpopulations

Gnomad4 AFR

AF:

0.684

Gnomad4 AMR

AF:

0.617

Gnomad4 ASJ

AF:

0.394

Gnomad4 EAS

AF:

0.798

Gnomad4 SAS

AF:

0.533

Gnomad4 FIN

AF:

0.690

Gnomad4 NFE

AF:

0.512

Gnomad4 OTH

AF:

0.548

Alfa

AF:

0.527

Hom.:

38102

Bravo

AF:

0.592

Asia WGS

AF:

0.699

AC:

2433

AN:

3478

EpiCase

AF:

0.490

EpiControl

AF:

0.492

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

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

-0.63

CADD

Benign

1.7

DANN

Benign

0.25

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

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