Variant 2-28906450-T-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP4_StrongBP6_Very_StrongBS2

The NM_015131.3(WDR43):c.364-10T>A variant causes a splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0129 in 1,482,772 control chromosomes in the GnomAD database, including 88 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.011 ( 16 hom., cov: 31)

Exomes 𝑓: 0.013 ( 72 hom. )

Consequence

WDR43
NM_015131.3 splice_polypyrimidine_tract, intron

Scores

Splicing: ADA: 0.05235

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: -0.0890

Variant links:

Genes affected

WDR43 (HGNC:28945): (WD repeat domain 43) Enables RNA binding activity. Involved in positive regulation of rRNA processing and positive regulation of transcription by RNA polymerase I. Located in fibrillar center. [provided by Alliance of Genome Resources, Apr 2022]

WDR43 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -16 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.74).

BP6

Variant 2-28906450-T-A is Benign according to our data. Variant chr2-28906450-T-A is described in ClinVar as [Benign]. Clinvar id is 777944.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BS2

High AC in GnomAd4 at 1614 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
WDR43	NM_015131.3 linkuse as main transcript	c.364-10T>A		splice_polypyrimidine_tract_variant, intron_variant		ENST00000407426.8

Ensembl

Gene	Transcript	HGVSc	Effect	TSL	MANE	Appris
WDR43	ENST00000407426.8 linkuse as main transcript	c.364-10T>A	splice_polypyrimidine_tract_variant, intron_variant	1	NM_015131.3	P1
WDR43	ENST00000296126.6 linkuse as main transcript	c.-180-10T>A	splice_polypyrimidine_tract_variant, intron_variant	5
WDR43	ENST00000440983.1 linkuse as main transcript	c.97-10T>A	splice_polypyrimidine_tract_variant, intron_variant	4

Frequencies

GnomAD3 genomes

AF:

0.0110

AC:

1615

AN:

146636

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00336

Gnomad AMI

AF:

0.0179

Gnomad AMR

AF:

0.0128

Gnomad ASJ

AF:

0.0105

Gnomad EAS

AF:

0.00241

Gnomad SAS

AF:

0.00109

Gnomad FIN

AF:

0.0215

Gnomad MID

AF:

0.0190

Gnomad NFE

AF:

0.0149

Gnomad OTH

AF:

0.0103

GnomAD3 exomes

AF:

0.0112

AC:

1366

AN:

121870

Hom.:

AF XY:

0.0107

AC XY:

689

AN XY:

64398

show subpopulations

Gnomad AFR exome

AF:

0.00235

Gnomad AMR exome

AF:

0.00991

Gnomad ASJ exome

AF:

0.0121

Gnomad EAS exome

AF:

0.00185

Gnomad SAS exome

AF:

0.00188

Gnomad FIN exome

AF:

0.0183

Gnomad NFE exome

AF:

0.0153

Gnomad OTH exome

AF:

0.0134

GnomAD4 exome

AF:

0.0131

AC:

17528

AN:

1336028

Hom.:

Cov.:

AF XY:

0.0127

AC XY:

8394

AN XY:

658494

show subpopulations

Gnomad4 AFR exome

AF:

0.00243

Gnomad4 AMR exome

AF:

0.0104

Gnomad4 ASJ exome

AF:

0.0116

Gnomad4 EAS exome

AF:

0.00124

Gnomad4 SAS exome

AF:

0.00221

Gnomad4 FIN exome

AF:

0.0195

Gnomad4 NFE exome

AF:

0.0144

Gnomad4 OTH exome

AF:

0.0122

GnomAD4 genome

AF:

0.0110

AC:

1614

AN:

146744

Hom.:

Cov.:

AF XY:

0.0110

AC XY:

788

AN XY:

71348

show subpopulations

Gnomad4 AFR

AF:

0.00335

Gnomad4 AMR

AF:

0.0127

Gnomad4 ASJ

AF:

0.0105

Gnomad4 EAS

AF:

0.00242

Gnomad4 SAS

AF:

0.00131

Gnomad4 FIN

AF:

0.0215

Gnomad4 NFE

AF:

0.0149

Gnomad4 OTH

AF:

0.0102

Alfa

AF:

0.0139

Hom.:

Bravo

AF:

0.00947

ClinVar

Significance: Benign

Submissions summary: Benign:2

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	Labcorp Genetics (formerly Invitae), Labcorp	Aug 24, 2017	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.74

CADD

Benign

0.091

DANN

Benign

0.82

Splicing

Name

Calibrated prediction

Score

Prediction

dbscSNV1_ADA

Benign

0.052

dbscSNV1_RF

Benign

0.39

SpliceAI score (max)

0.030

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