Variant 1-111443384-C-A 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_024102.4(WDR77):c.630G>T(p.Ala210Ala) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00599 in 1,552,362 control chromosomes in the GnomAD database, including 49 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.0037 ( 1 hom., cov: 32)

Exomes 𝑓: 0.0062 ( 48 hom. )

Consequence

WDR77
NM_024102.4 synonymous

Scores

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.953

Variant links:

Genes affected

WDR77 (HGNC:29652): (WD repeat domain 77) The protein encoded by this gene is an androgen receptor coactivator that forms a complex with protein arginine methyltransferase 5, which modifies specific arginines to dimethylarginines in several spliceosomal Sm proteins. The encoded protein may be involved in the early stages of prostate cancer, with most of the protein being nuclear-localized in benign cells but cytoplasmic in cancer cells. Several transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Nov 2015]

WDR77 links:

WDR77 (HGNC:):

WDR77 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -9 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.24).

BP6

Variant 1-111443384-C-A is Benign according to our data. Variant chr1-111443384-C-A is described in ClinVar as [Likely_benign]. Clinvar id is 2638993.Status of the report is criteria_provided_single_submitter, 1 stars.

BP7

Synonymous conserved (PhyloP=0.953 with no splicing effect.

BS2

High Homozygotes in GnomAdExome4 at 48 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
WDR77	NM_024102.4 linkuse as main transcript	c.630G>T	p.Ala210Ala	synonymous_variant	7/10	ENST00000235090.10	NP_077007.1	Q9BQA1-1A0A024R0H7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	UniProt
WDR77	ENST00000235090.10 linkuse as main transcript	c.630G>T	p.Ala210Ala	synonymous_variant	7/10	1	NM_024102.4	ENSP00000235090.5	Q9BQA1-1
WDR77	ENST00000449340.1 linkuse as main transcript	c.438G>T	p.Ala146Ala	synonymous_variant	6/9	5		ENSP00000409300.1	H0Y711
WDR77	ENST00000459665.1 linkuse as main transcript	n.602G>T		non_coding_transcript_exon_variant	6/6	3
WDR77	ENST00000497278.5 linkuse as main transcript	n.285G>T		non_coding_transcript_exon_variant	5/9	3

Frequencies

GnomAD3 genomes

AF:

0.00371

AC:

565

AN:

152188

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00164

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00210

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00352

Gnomad FIN

AF:

0.000377

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00644

Gnomad OTH

AF:

0.00287

GnomAD3 exomes

AF:

0.00346

AC:

545

AN:

157688

Hom.:

AF XY:

0.00360

AC XY:

299

AN XY:

82972

show subpopulations

Gnomad AFR exome

AF:

0.000787

Gnomad AMR exome

AF:

0.00141

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.00425

Gnomad FIN exome

AF:

0.000455

Gnomad NFE exome

AF:

0.00628

Gnomad OTH exome

AF:

0.00315

GnomAD4 exome

AF:

0.00624

AC:

8737

AN:

1400056

Hom.:

Cov.:

AF XY:

0.00617

AC XY:

4258

AN XY:

690628

show subpopulations

Gnomad4 AFR exome

AF:

0.000663

Gnomad4 AMR exome

AF:

0.00137

Gnomad4 ASJ exome

AF:

0.00

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.00368

Gnomad4 FIN exome

AF:

0.000872

Gnomad4 NFE exome

AF:

0.00746

Gnomad4 OTH exome

AF:

0.00475

GnomAD4 genome

AF:

0.00372

AC:

566

AN:

152306

Hom.:

Cov.:

AF XY:

0.00340

AC XY:

253

AN XY:

74470

show subpopulations

Gnomad4 AFR

AF:

0.00164

Gnomad4 AMR

AF:

0.00209

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00373

Gnomad4 FIN

AF:

0.000377

Gnomad4 NFE

AF:

0.00644

Gnomad4 OTH

AF:

0.00284

Alfa

AF:

0.00386

Hom.:

Bravo

AF:

0.00376

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

Dec 01, 2022

WDR77: BP4, BP7, BS2 -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.24

CADD

Benign

2.3

DANN

Benign

0.64

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.7

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.020

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