rs370267621

Variant names:

• chr12-65056267-CTTTT-C
• rs370267621
• NM_007191.5:c.827-145_827-142delAAAA

Your query was ambiguous. Multiple possible variants found:

• chr12-65056267-CTTTT-C
• chr12-65056267-CTTTT-CT
• chr12-65056267-CTTTT-CTT
• chr12-65056267-CTTTT-CTTT
• chr12-65056267-CTTTT-CTTTTT
• chr12-65056267-CTTTT-CTTTTTT
• chr12-65056267-CTTTT-CTTTTTTT

Variant summary

Our verdict is Uncertain significance. The variant received 2 ACMG points: 2P and 0B. PM2

The NM_007191.5(WIF1):​c.827-145_827-142delAAAA variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000821 in 486,996 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 0.0000085 (0 hom., cov: 31)
  • Exomes 𝑓: 0.0000081 (0 hom.)
• Consequence: WIF1 NM_007191.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.28
• Publications: 0 publications found

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]

ACMG classification

Our verdict: Uncertain_significance. The variant received 2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage

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.827-145_827-142delAAAA		intron	N/A	NP_009122.2	Q9Y5W5

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	WIF1	ENST00000286574.9	TSL:1 MANE Select	c.827-145_827-142delAAAA		intron	N/A	ENSP00000286574.4	Q9Y5W5
	WIF1	ENST00000954483.1		c.797-145_797-142delAAAA		intron	N/A	ENSP00000624542.1
	WIF1	ENST00000954485.1		c.827-175_827-172delAAAA		intron	N/A	ENSP00000624544.1

Frequencies

GnomAD3 genomes AF: 0.00000847 AC: 1 AN: 118012 Hom.: 0 Cov.: 31

Gnomad AFR AF: 0.00

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00

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: 0.00000813 AC: 3 AN: 368984 Hom.: 0 AF XY: 0.00000523 AC XY: 1 AN XY: 191220

African (AFR) AF: 0.00 AC: 0 AN: 9458

American (AMR) AF: 0.00 AC: 0 AN: 9760

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 9006

East Asian (EAS) AF: 0.00 AC: 0 AN: 20264

South Asian (SAS) AF: 0.00 AC: 0 AN: 27312

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 21022

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 2044

European-Non Finnish (NFE) AF: 0.0000120 AC: 3 AN: 250830

Other (OTH) AF: 0.00 AC: 0 AN: 19288

GnomAD4 genome AF: 0.00000847 AC: 1 AN: 118012 Hom.: 0 Cov.: 31 AF XY: 0.0000178 AC XY: 1 AN XY: 56138

African (AFR) AF: 0.00 AC: 0 AN: 33676

American (AMR) AF: 0.00 AC: 0 AN: 10968

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 2914

East Asian (EAS) AF: 0.00 AC: 0 AN: 3872

South Asian (SAS) AF: 0.00 AC: 0 AN: 3774

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 5262

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 152

European-Non Finnish (NFE) AF: 0.0000181 AC: 1 AN: 55110

Other (OTH) AF: 0.00 AC: 0 AN: 1564

Alfa AF: 0.00 Hom.: 1

Bravo AF: 0.00000756

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		2.3

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

Other links and lift over

dbSNP: rs370267621; hg19: chr12-65450047;