Genetic Variant WIF1:c.827-142delA (chr12-65056267-CT-C) – ACMG Classification: Benign (-8 pts)

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1

The NM_007191.5(WIF1):c.827-142delA variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0814 in 448,948 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.00099 ( 0 hom., cov: 31)

Exomes 𝑓: 0.11 ( 0 hom. )

Consequence

WIF1
NM_007191.5 intron

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 2.28

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:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -8 ACMG points.

BA1

GnomAdExome4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.139 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
WIF1	NM_007191.5 link	c.827-142delA		intron_variant	Intron 7 of 9	ENST00000286574.9	NP_009122.2	Q9Y5W5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
WIF1	ENST00000286574.9 link	c.827-142delA		intron_variant	Intron 7 of 9	1	NM_007191.5	ENSP00000286574.4		Q9Y5W5
WIF1	ENST00000543094.1 link	c.116-142delA		intron_variant	Intron 2 of 4	5		ENSP00000439024.1		H0YFK7

Frequencies

GnomAD3 genomes

AF:

0.000993

AC:

117

AN:

117860

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00104

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00128

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00181

Gnomad SAS

AF:

0.000530

Gnomad FIN

AF:

0.00420

Gnomad MID

AF:

0.00658

Gnomad NFE

AF:

0.000618

Gnomad OTH

AF:

0.00128

GnomAD4 exome

AF:

0.110

AC:

36435

AN:

331078

Hom.:

AF XY:

0.112

AC XY:

19202

AN XY:

171116

show subpopulations

Gnomad4 AFR exome

AF:

0.0805

Gnomad4 AMR exome

AF:

0.143

Gnomad4 ASJ exome

AF:

0.132

Gnomad4 EAS exome

AF:

0.143

Gnomad4 SAS exome

AF:

0.119

Gnomad4 FIN exome

AF:

0.118

Gnomad4 NFE exome

AF:

0.104

Gnomad4 OTH exome

AF:

0.120

GnomAD4 genome

AF:

0.000993

AC:

117

AN:

117870

Hom.:

Cov.:

AF XY:

0.000963

AC XY:

AN XY:

56072

show subpopulations

Gnomad4 AFR

AF:

0.00107

Gnomad4 AMR

AF:

0.00128

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.00182

Gnomad4 SAS

AF:

0.000266

Gnomad4 FIN

AF:

0.00420

Gnomad4 NFE

AF:

0.000618

Gnomad4 OTH

AF:

0.00128

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

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.

12-65056267-CTTTT-CTTT

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over