Variant 10-28534197-G-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1

The NM_016628.5(WAC):c.78+163G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.266 in 629,680 control chromosomes in the GnomAD database, including 23,640 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.23 ( 4690 hom., cov: 32)

Exomes 𝑓: 0.28 ( 18950 hom. )

Consequence

WAC
NM_016628.5 intron

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.994

Variant links:

Genes affected

WAC (HGNC:17327): (WW domain containing adaptor with coiled-coil) The protein encoded by this gene contains a WW domain, which is a protein module found in a wide range of signaling proteins. This domain mediates protein-protein interactions and binds proteins containing short linear peptide motifs that are proline-rich or contain at least one proline. This gene product shares 94% sequence identity with the WAC protein in mouse, however, its exact function is not known. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Dec 2008]

WAC links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.81).

BP6

Variant 10-28534197-G-A is Benign according to our data. Variant chr10-28534197-G-A is described in ClinVar as [Benign]. Clinvar id is 1278808.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.275 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
WAC	NM_016628.5 linkuse as main transcript	c.78+163G>A		intron_variant		ENST00000354911.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
WAC	ENST00000354911.9 linkuse as main transcript	c.78+163G>A		intron_variant		1	NM_016628.5	P3	Q9BTA9-1

Frequencies

GnomAD3 genomes

AF:

0.225

AC:

34235

AN:

151946

Hom.:

4689

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0760

Gnomad AMI

AF:

0.426

Gnomad AMR

AF:

0.245

Gnomad ASJ

AF:

0.265

Gnomad EAS

AF:

0.255

Gnomad SAS

AF:

0.218

Gnomad FIN

AF:

0.406

Gnomad MID

AF:

0.0981

Gnomad NFE

AF:

0.278

Gnomad OTH

AF:

0.226

GnomAD3 exomes

AF:

0.333

AC:

6748

AN:

20268

Hom.:

1083

AF XY:

0.327

AC XY:

3531

AN XY:

10790

show subpopulations

Gnomad AFR exome

AF:

0.0980

Gnomad AMR exome

AF:

0.270

Gnomad ASJ exome

AF:

0.339

Gnomad EAS exome

AF:

0.291

Gnomad SAS exome

AF:

0.285

Gnomad FIN exome

AF:

0.411

Gnomad NFE exome

AF:

0.316

Gnomad OTH exome

AF:

0.277

GnomAD4 exome

AF:

0.279

AC:

133477

AN:

477614

Hom.:

18950

Cov.:

AF XY:

0.278

AC XY:

68239

AN XY:

245718

show subpopulations

Gnomad4 AFR exome

AF:

0.0758

Gnomad4 AMR exome

AF:

0.251

Gnomad4 ASJ exome

AF:

0.263

Gnomad4 EAS exome

AF:

0.235

Gnomad4 SAS exome

AF:

0.233

Gnomad4 FIN exome

AF:

0.407

Gnomad4 NFE exome

AF:

0.283

Gnomad4 OTH exome

AF:

0.260

GnomAD4 genome

AF:

0.225

AC:

34240

AN:

152066

Hom.:

4690

Cov.:

AF XY:

0.230

AC XY:

17110

AN XY:

74332

show subpopulations

Gnomad4 AFR

AF:

0.0761

Gnomad4 AMR

AF:

0.245

Gnomad4 ASJ

AF:

0.265

Gnomad4 EAS

AF:

0.254

Gnomad4 SAS

AF:

0.217

Gnomad4 FIN

AF:

0.406

Gnomad4 NFE

AF:

0.278

Gnomad4 OTH

AF:

0.223

Alfa

AF:

0.207

Hom.:

779

Bravo

AF:

0.208

Asia WGS

AF:

0.233

AC:

809

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Jul 26, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.81

Cadd

Benign

Dann

Benign

0.53

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.090

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