Genetic Variant WIF1:c.827-143_827-142dupAA (chr12-65056267-C-CTT) – ACMG Classification: Uncertain_significance (0 pts)

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 0P and 0B.

The NM_007191.5(WIF1):c.827-143_827-142dupAA variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00023 in 486,516 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 0.00016 ( 0 hom., cov: 31)

Exomes 𝑓: 0.00025 ( 0 hom. )

Consequence

WIF1
NM_007191.5 intron

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 2.28

Publications

0 publications found

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 was made for transcript

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_007191.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	WIF1	NM_007191.5	MANE Select	c.827-143_827-142dupAA		intron	N/A	NP_009122.2	Q9Y5W5

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
WIF1	ENST00000286574.9	TSL:1 MANE Select	c.827-142_827-141insAA	intron	N/A	ENSP00000286574.4	Q9Y5W5
WIF1	ENST00000954483.1		c.797-142_797-141insAA	intron	N/A	ENSP00000624542.1
WIF1	ENST00000954485.1		c.827-172_827-171insAA	intron	N/A	ENSP00000624544.1

Frequencies

GnomAD3 genomes

AF:

0.000161

AC:

AN:

118012

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000505

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0000912

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.0000181

Gnomad OTH

AF:

0.00

GnomAD4 exome

AF:

0.000252

AC:

AN:

368494

Hom.:

AF XY:

0.000272

AC XY:

AN XY:

190954

show subpopulations

⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.

African (AFR)

AF:

0.00202

AC:

AN:

9412

American (AMR)

AF:

0.000205

AC:

AN:

9738

Ashkenazi Jewish (ASJ)

AF:

0.000111

AC:

AN:

8988

East Asian (EAS)

AF:

0.000544

AC:

AN:

20224

South Asian (SAS)

AF:

0.000770

AC:

AN:

27270

European-Finnish (FIN)

AF:

0.0000476

AC:

AN:

21002

Middle Eastern (MID)

AF:

0.00

AC:

AN:

2040

European-Non Finnish (NFE)

AF:

0.000128

AC:

AN:

250552

Other (OTH)

AF:

0.000311

AC:

AN:

19268

⚠️ The allele balance in gnomAD4 Exomes is highly skewed from 0.5 (p-value = 0), which strongly suggests a high chance of mosaicism in these individuals.

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.267

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.000161

AC:

AN:

118022

Hom.:

Cov.:

AF XY:

0.000178

AC XY:

AN XY:

56172

show subpopulations

African (AFR)

AF:

0.000504

AC:

AN:

33726

American (AMR)

AF:

0.0000912

AC:

AN:

10968

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

2914

East Asian (EAS)

AF:

0.00

AC:

AN:

3862

South Asian (SAS)

AF:

0.00

AC:

AN:

3756

European-Finnish (FIN)

AF:

0.00

AC:

AN:

5262

Middle Eastern (MID)

AF:

0.00

AC:

AN:

142

European-Non Finnish (NFE)

AF:

0.0000181

AC:

AN:

55104

Other (OTH)

AF:

0.00

AC:

AN:

1568

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.496

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.00

Hom.:

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

PhyloP100

2.3

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over