Variant chr1-108974747-T-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_ModerateBP6_ModerateBP7BS2

The NM_001142551.2(WDR47):c.2406A>G(p.Ala802Ala) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00134 in 1,608,980 control chromosomes in the GnomAD database, including 9 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.0022 ( 1 hom., cov: 33)

Exomes 𝑓: 0.0012 ( 8 hom. )

Consequence

WDR47
NM_001142551.2 synonymous

Scores

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.0810

Variant links:

Genes affected

WDR47 (HGNC:29141): (WD repeat domain 47) Predicted to be located in cytoplasm and microtubule. [provided by Alliance of Genome Resources, Apr 2022]

WDR47 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -9 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.46).

BP6

Variant 1-108974747-T-C is Benign according to our data. Variant chr1-108974747-T-C is described in ClinVar as [Likely_benign]. Clinvar id is 2638966.Status of the report is criteria_provided_single_submitter, 1 stars.

BP7

Synonymous conserved (PhyloP=0.081 with no splicing effect.

BS2

High AC in GnomAd4 at 335 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
WDR47	NM_001142551.2 linkuse as main transcript	c.2406A>G	p.Ala802Ala	synonymous_variant	14/15	ENST00000369962.8	NP_001136023.1	O94967-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	UniProt
WDR47	ENST00000369962.8 linkuse as main transcript	c.2406A>G	p.Ala802Ala	synonymous_variant	14/15	1	NM_001142551.2	ENSP00000358979.3	O94967-1
WDR47	ENST00000400794.7 linkuse as main transcript	c.2430A>G	p.Ala810Ala	synonymous_variant	14/15	1		ENSP00000383599.3	O94967-4
WDR47	ENST00000369965.8 linkuse as main transcript	c.2409A>G	p.Ala803Ala	synonymous_variant	14/15	1		ENSP00000358982.4	O94967-3
WDR47	ENST00000361054.7 linkuse as main transcript	c.2322A>G	p.Ala774Ala	synonymous_variant	13/14	5		ENSP00000354339.3	O94967-2

Frequencies

GnomAD3 genomes

AF:

0.00219

AC:

334

AN:

152208

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00273

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.000262

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.000207

Gnomad FIN

AF:

0.00311

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00266

Gnomad OTH

AF:

0.000957

GnomAD3 exomes

AF:

0.00174

AC:

418

AN:

240442

Hom.:

AF XY:

0.00176

AC XY:

228

AN XY:

129768

show subpopulations

Gnomad AFR exome

AF:

0.00257

Gnomad AMR exome

AF:

0.000121

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.00

Gnomad FIN exome

AF:

0.00461

Gnomad NFE exome

AF:

0.00250

Gnomad OTH exome

AF:

0.00117

GnomAD4 exome

AF:

0.00125

AC:

1815

AN:

1456654

Hom.:

Cov.:

AF XY:

0.00130

AC XY:

943

AN XY:

724112

show subpopulations

Gnomad4 AFR exome

AF:

0.00294

Gnomad4 AMR exome

AF:

0.0000916

Gnomad4 ASJ exome

AF:

0.00

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.0000351

Gnomad4 FIN exome

AF:

0.00436

Gnomad4 NFE exome

AF:

0.00124

Gnomad4 OTH exome

AF:

0.00163

GnomAD4 genome

AF:

0.00220

AC:

335

AN:

152326

Hom.:

Cov.:

AF XY:

0.00204

AC XY:

152

AN XY:

74506

show subpopulations

Gnomad4 AFR

AF:

0.00274

Gnomad4 AMR

AF:

0.000262

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.000207

Gnomad4 FIN

AF:

0.00311

Gnomad4 NFE

AF:

0.00266

Gnomad4 OTH

AF:

0.000947

Alfa

AF:

0.00270

Hom.:

Bravo

AF:

0.00175

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Likely benign, criteria provided, single submitter

clinical testing

CeGaT Center for Human Genetics Tuebingen

Aug 01, 2022

WDR47: BP4, BP7 -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.46

CADD

Benign

6.7

DANN

Benign

0.74

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