Variant 9-16848-G-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -7 ACMG points: 0P and 7B. BP4_StrongBP6_ModerateBP7

The NM_001378090.1(WASHC1):c.912C>A(p.Pro304Pro) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.0013 ( 0 hom., cov: 5)

Exomes 𝑓: 0.015 ( 9 hom. )

Failed GnomAD Quality Control

Consequence

WASHC1
NM_001378090.1 synonymous

Scores

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: -1.65

Variant links:

Genes affected

WASHC1 (HGNC:24361): (WASH complex subunit 1) Enables alpha-tubulin binding activity and ubiquitin protein ligase binding activity. Involved in several processes, including Arp2/3 complex-mediated actin nucleation; endosomal transport; and positive regulation of pseudopodium assembly. Located in early endosome. Part of WASH complex. Colocalizes with exocyst. [provided by Alliance of Genome Resources, Apr 2022]

WASHC1 links:

WASHC1 (HGNC:):

WASHC1 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -7 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.68).

BP6

Variant 9-16848-G-T is Benign according to our data. Variant chr9-16848-G-T is described in ClinVar as [Likely_benign]. Clinvar id is 2659007.Status of the report is criteria_provided_single_submitter, 1 stars.

BP7

Synonymous conserved (PhyloP=-1.65 with no splicing effect.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
WASHC1	NM_001378090.1 linkuse as main transcript	c.912C>A	p.Pro304Pro	synonymous_variant	8/11	ENST00000696149.1	NP_001365019.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
WASHC1	ENST00000696149.1 linkuse as main transcript	c.912C>A	p.Pro304Pro	synonymous_variant	8/11		NM_001378090.1	ENSP00000512441.1		A8K0Z3

Frequencies

GnomAD3 genomes

AF:

0.00

AC:

AN:

30260

Hom.:

Cov.:

FAILED QC

Gnomad AFR

AF:

0.00245

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.000347

Gnomad ASJ

AF:

0.00114

Gnomad EAS

AF:

0.00473

Gnomad SAS

AF:

0.00159

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00113

Gnomad OTH

AF:

0.00

GnomAD3 exomes

AF:

0.00138

AC:

AN:

60986

Hom.:

AF XY:

0.00149

AC XY:

AN XY:

31602

show subpopulations

Gnomad AFR exome

AF:

0.000979

Gnomad AMR exome

AF:

0.00115

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.00638

Gnomad SAS exome

AF:

0.000950

Gnomad FIN exome

AF:

0.00136

Gnomad NFE exome

AF:

0.000518

Gnomad OTH exome

AF:

0.00142

GnomAD4 exome

Data not reliable, filtered out with message: AS_VQSR

AF:

0.0154

AC:

6291

AN:

408662

Hom.:

Cov.:

AF XY:

0.0155

AC XY:

3358

AN XY:

217284

show subpopulations

Gnomad4 AFR exome

AF:

0.0197

Gnomad4 AMR exome

AF:

0.0184

Gnomad4 ASJ exome

AF:

0.0154

Gnomad4 EAS exome

AF:

0.0114

Gnomad4 SAS exome

AF:

0.0209

Gnomad4 FIN exome

AF:

0.00912

Gnomad4 NFE exome

AF:

0.0145

Gnomad4 OTH exome

AF:

0.0166

GnomAD4 genome

Data not reliable, filtered out with message: AS_VQSR

AF:

0.00129

AC:

AN:

30324

Hom.:

Cov.:

AF XY:

0.00147

AC XY:

AN XY:

13592

show subpopulations

Gnomad4 AFR

AF:

0.00243

Gnomad4 AMR

AF:

0.000346

Gnomad4 ASJ

AF:

0.00114

Gnomad4 EAS

AF:

0.00476

Gnomad4 SAS

AF:

0.00158

Gnomad4 FIN

AF:

0.00

Gnomad4 NFE

AF:

0.00113

Gnomad4 OTH

AF:

0.00

Alfa

AF:

0.00506

Hom.:

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

Oct 01, 2022

WASHC1: BP4, BP7 -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.68

CADD

Benign

0.0030

DANN

Benign

0.69

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