Variant 2-174566979-C-G details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The ENST00000409891.5(WIPF1):c.*65G>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.518 in 1,281,682 control chromosomes in the GnomAD database, including 177,513 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.49 ( 19193 hom., cov: 32)

Exomes 𝑓: 0.52 ( 158320 hom. )

Consequence

WIPF1
ENST00000409891.5 3_prime_UTR

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: -0.330

Variant links:

Genes affected

WIPF1 (HGNC:12736): (WAS/WASL interacting protein family member 1) This gene encodes a protein that plays an important role in the organization of the actin cytoskeleton. The encoded protein binds to a region of Wiskott-Aldrich syndrome protein that is frequently mutated in Wiskott-Aldrich syndrome, an X-linked recessive disorder. Impairment of the interaction between these two proteins may contribute to the disease. Two transcript variants encoding the same protein have been identified for this gene. [provided by RefSeq, Jul 2008]

WIPF1 links:

(HGNC:):

links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.82).

BP6

Variant 2-174566979-C-G is Benign according to our data. Variant chr2-174566979-C-G is described in ClinVar as [Benign]. Clinvar id is 1263797.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.832 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
WIPF1	NM_001375834.1 linkuse as main transcript	c.1456+91G>C		intron_variant		ENST00000679041.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
WIPF1	ENST00000679041.1 linkuse as main transcript	c.1456+91G>C		intron_variant			NM_001375834.1	P3	O43516-1
	ENST00000442996.1 linkuse as main transcript	n.217+19502C>G		intron_variant, non_coding_transcript_variant		1

Frequencies

GnomAD3 genomes

AF:

0.489

AC:

74245

AN:

151898

Hom.:

19195

Cov.:

show subpopulations

Gnomad AFR

AF:

0.336

Gnomad AMI

AF:

0.542

Gnomad AMR

AF:

0.546

Gnomad ASJ

AF:

0.669

Gnomad EAS

AF:

0.853

Gnomad SAS

AF:

0.508

Gnomad FIN

AF:

0.599

Gnomad MID

AF:

0.516

Gnomad NFE

AF:

0.511

Gnomad OTH

AF:

0.525

GnomAD4 exome

AF:

0.522

AC:

590046

AN:

1129666

Hom.:

158320

Cov.:

AF XY:

0.522

AC XY:

297832

AN XY:

570704

show subpopulations

Gnomad4 AFR exome

AF:

0.333

Gnomad4 AMR exome

AF:

0.622

Gnomad4 ASJ exome

AF:

0.663

Gnomad4 EAS exome

AF:

0.857

Gnomad4 SAS exome

AF:

0.506

Gnomad4 FIN exome

AF:

0.586

Gnomad4 NFE exome

AF:

0.502

Gnomad4 OTH exome

AF:

0.530

GnomAD4 genome

AF:

0.489

AC:

74261

AN:

152016

Hom.:

19193

Cov.:

AF XY:

0.493

AC XY:

36627

AN XY:

74296

show subpopulations

Gnomad4 AFR

AF:

0.336

Gnomad4 AMR

AF:

0.546

Gnomad4 ASJ

AF:

0.669

Gnomad4 EAS

AF:

0.853

Gnomad4 SAS

AF:

0.507

Gnomad4 FIN

AF:

0.599

Gnomad4 NFE

AF:

0.511

Gnomad4 OTH

AF:

0.522

Alfa

AF:

0.486

Hom.:

2297

Bravo

AF:

0.481

Asia WGS

AF:

0.578

AC:

2011

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not specified

Benign:1

Benign, criteria provided, single submitter

clinical testing

Unidad de Genómica Garrahan, Hospital de Pediatría Garrahan

Jan 24, 2024

This variant is classified as Benign based on local population frequency. This variant was detected in 82% of patients studied by a panel of primary immunodeficiencies. Number of patients: 72. Only high quality variants are reported. -

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Nov 12, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.82

CADD

Benign

1.7

DANN

Benign

0.45

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

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over