NM_020830.5:c.138-11851_138-11850insCT

Variant names:

• chr2-223929860-C-CAG
• rs1160893
• NM_020830.5:c.138-11851_138-11850insCT

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BA1

The NM_020830.5(WDFY1):​c.138-11851_138-11850insCT variant causes a intron change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.84 (54468 hom., cov: 0)
• Consequence: WDFY1 NM_020830.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.00
• Publications: 2 publications found

Genes affected

WDFY1 (HGNC:20451): (WD repeat and FYVE domain containing 1) The protein encoded by this gene is a phosphatidylinositol 3-phosphate binding protein, which contains a FYVE zinc finger domain and multiple WD-40 repeat domains. When exogenously expressed, it localizes to early endosomes. Mutagenesis analysis demonstrates that this endosomal localization is mediated by the FYVE domain. [provided by RefSeq, Jan 2015]

ENSG00000286239 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -8 ACMG points.

• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.921 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
WDFY1	NM_020830.5	c.138-11851_138-11850insCT		intron_variant	Intron 1 of 11	ENST00000233055.9	NP_065881.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
WDFY1	ENST00000233055.9	c.138-11851_138-11850insCT		intron_variant	Intron 1 of 11	1	NM_020830.5	ENSP00000233055.4
ENSG00000286239	ENST00000650969.1	n.138-11851_138-11850insCT		intron_variant	Intron 1 of 16			ENSP00000498456.1
WDFY1	ENST00000429915.1	c.138-11851_138-11850insCT		intron_variant	Intron 1 of 5	3		ENSP00000395416.1
WDFY1	ENST00000483061.1	n.189-11851_189-11850insCT		intron_variant	Intron 1 of 4	2

Frequencies

GnomAD3 genomes AF: 0.841 AC: 127718 AN: 151848 Hom.: 54442 Cov.: 0

Gnomad AFR AF: 0.724

Gnomad AMI AF: 0.974

Gnomad AMR AF: 0.845

Gnomad ASJ AF: 0.875

Gnomad EAS AF: 0.542

Gnomad SAS AF: 0.865

Gnomad FIN AF: 0.853

Gnomad MID AF: 0.899

Gnomad NFE AF: 0.927

Gnomad OTH AF: 0.840

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.841 AC: 127796 AN: 151966 Hom.: 54468 Cov.: 0 AF XY: 0.835 AC XY: 62018 AN XY: 74262

African (AFR) AF: 0.724 AC: 29955 AN: 41376

American (AMR) AF: 0.844 AC: 12896 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.875 AC: 3037 AN: 3472

East Asian (EAS) AF: 0.542 AC: 2792 AN: 5152

South Asian (SAS) AF: 0.865 AC: 4172 AN: 4822

European-Finnish (FIN) AF: 0.853 AC: 8999 AN: 10552

Middle Eastern (MID) AF: 0.888 AC: 261 AN: 294

European-Non Finnish (NFE) AF: 0.927 AC: 63034 AN: 68000

Other (OTH) AF: 0.834 AC: 1764 AN: 2116

Alfa AF: 0.881 Hom.: 7232

Bravo AF: 0.833

Asia WGS AF: 0.691 AC: 2406 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
PhyloP100		2.0
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs1160893; hg19: chr2-224794577;