Variant 12-65055206-G-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1

The NM_007191.5(WIF1):c.930C>T(p.Cys310=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0107 in 1,613,390 control chromosomes in the GnomAD database, including 990 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.012 ( 115 hom., cov: 33)

Exomes 𝑓: 0.011 ( 875 hom. )

Consequence

WIF1
NM_007191.5 synonymous

Scores

Clinical Significance

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

Conservation

PhyloP100: -0.432

Variant links:

Genes affected

WIF1 (HGNC:18081): (WNT inhibitory factor 1) The protein encoded by this gene functions to inhibit WNT proteins, which are extracellular signaling molecules that play a role in embryonic development. This protein contains a WNT inhibitory factor (WIF) domain and five epidermal growth factor (EGF)-like domains, and is thought to be involved in mesoderm segmentation. This gene functions as a tumor suppressor gene, and has been found to be epigenetically silenced in various cancers. [provided by RefSeq, Jun 2010]

WIF1 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -21 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.6).

BP6

Variant 12-65055206-G-A is Benign according to our data. Variant chr12-65055206-G-A is described in ClinVar as [Benign]. Clinvar id is 1236341.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=-0.432 with no splicing effect.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.166 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
WIF1	NM_007191.5 linkuse as main transcript	c.930C>T	p.Cys310=	synonymous_variant	9/10	ENST00000286574.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
WIF1	ENST00000286574.9 linkuse as main transcript	c.930C>T	p.Cys310=	synonymous_variant	9/10	1	NM_007191.5	P1
WIF1	ENST00000543094.1 linkuse as main transcript	c.177C>T	p.Cys59=	synonymous_variant	4/5	5

Frequencies

GnomAD3 genomes

AF:

0.0123

AC:

1876

AN:

152138

Hom.:

116

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00285

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0274

Gnomad ASJ

AF:

0.00115

Gnomad EAS

AF:

0.176

Gnomad SAS

AF:

0.0743

Gnomad FIN

AF:

0.0000944

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.000426

Gnomad OTH

AF:

0.0158

GnomAD3 exomes

AF:

0.0303

AC:

7592

AN:

250564

Hom.:

477

AF XY:

0.0289

AC XY:

3917

AN XY:

135382

show subpopulations

Gnomad AFR exome

AF:

0.00246

Gnomad AMR exome

AF:

0.0627

Gnomad ASJ exome

AF:

0.00219

Gnomad EAS exome

AF:

0.183

Gnomad SAS exome

AF:

0.0601

Gnomad FIN exome

AF:

0.000185

Gnomad NFE exome

AF:

0.000538

Gnomad OTH exome

AF:

0.0199

GnomAD4 exome

AF:

0.0105

AC:

15357

AN:

1461134

Hom.:

875

Cov.:

AF XY:

0.0116

AC XY:

8429

AN XY:

726818

show subpopulations

Gnomad4 AFR exome

AF:

0.00152

Gnomad4 AMR exome

AF:

0.0578

Gnomad4 ASJ exome

AF:

0.00168

Gnomad4 EAS exome

AF:

0.148

Gnomad4 SAS exome

AF:

0.0602

Gnomad4 FIN exome

AF:

0.000225

Gnomad4 NFE exome

AF:

0.000316

Gnomad4 OTH exome

AF:

0.0209

GnomAD4 genome

AF:

0.0123

AC:

1869

AN:

152256

Hom.:

115

Cov.:

AF XY:

0.0146

AC XY:

1086

AN XY:

74436

show subpopulations

Gnomad4 AFR

AF:

0.00284

Gnomad4 AMR

AF:

0.0272

Gnomad4 ASJ

AF:

0.00115

Gnomad4 EAS

AF:

0.175

Gnomad4 SAS

AF:

0.0742

Gnomad4 FIN

AF:

0.0000944

Gnomad4 NFE

AF:

0.000426

Gnomad4 OTH

AF:

0.0156

Alfa

AF:

0.00556

Hom.:

Bravo

AF:

0.0148

Asia WGS

AF:

0.125

AC:

434

AN:

3478

EpiCase

AF:

0.000273

EpiControl

AF:

0.000474

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	clinical testing	GeneDx	May 05, 2021	- -
Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.60

CADD

Benign

5.8

DANN

Benign

0.56

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