Variant 12-65056267-CTTTT-CTTT details in Genebe, Genetics Data Aggregator

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.

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