Genetic Variant WASF4P:n.278T>G (chrX-47803573-T-G) – ACMG Classification: Likely_benign (-4 pts)

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_Strong

The ENST00000811713.1(ENSG00000305567):n.446A>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.59 ( 13864 hom., 19015 hem., cov: 23)

Exomes 𝑓: 0.59 ( 126816 hom. 209530 hem. )

Failed GnomAD Quality Control

Consequence

ENSG00000305567
ENST00000811713.1 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.813

Publications

10 publications found

Variant links:

Genes affected

WASF4P (HGNC:20801): (WASP family member 4, pseudogene) This gene is a pseudogene belonging to the family of genes encoding Wiskott-Aldrich syndrome (WAS) proteins, which are involved in the transmission of signals to the actin cytoskeleton. Wiskott-Aldrich syndrome is a disease of the immune system. This pseudogene, which is apparently not transcribed, most closely resembles the gene encoding the WAS protein family member 2, which is located on chromosome 1. [provided by RefSeq, Jul 2008]

WASF4P links:

ENSG00000305567 (HGNC:):

ENSG00000305567 links:

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new If you want to explore the variant's impact on the transcript ENST00000811713.1, check out the Mutation Effect Viewer. This is especially useful for frameshift variants or if you want to visualize the effect of exon loss / intron retention.

ACMG classification

Classification was made for transcript

Our verdict: Likely_benign. The variant received -4 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.61).

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000811713.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank
WASF4P	ENST00000444248.1	TSL:6	n.278T>G	non_coding_transcript_exon	Exon 1 of 1
ENSG00000305567	ENST00000811713.1		n.446A>C	non_coding_transcript_exon	Exon 4 of 4
ENSG00000305567	ENST00000811714.1		n.481A>C	non_coding_transcript_exon	Exon 4 of 4

Frequencies

GnomAD3 genomes

AF:

0.591

AC:

65202

AN:

110302

Hom.:

13864

Cov.:

show subpopulations

Gnomad AFR

AF:

0.605

Gnomad AMI

AF:

0.544

Gnomad AMR

AF:

0.627

Gnomad ASJ

AF:

0.558

Gnomad EAS

AF:

0.831

Gnomad SAS

AF:

0.572

Gnomad FIN

AF:

0.525

Gnomad MID

AF:

0.706

Gnomad NFE

AF:

0.570

Gnomad OTH

AF:

0.602

GnomAD2 exomes

AF:

0.611

AC:

111764

AN:

183001

AF XY:

0.607

show subpopulations

Gnomad AFR exome

AF:

0.613

Gnomad AMR exome

AF:

0.688

Gnomad ASJ exome

AF:

0.572

Gnomad EAS exome

AF:

0.835

Gnomad FIN exome

AF:

0.542

Gnomad NFE exome

AF:

0.571

Gnomad OTH exome

AF:

0.595

GnomAD4 exome

Data not reliable, filtered out with message: InbreedingCoeff

AF:

0.591

AC:

636977

AN:

1077758

Hom.:

126816

Cov.:

AF XY:

0.595

AC XY:

209530

AN XY:

351988

show subpopulations

African (AFR)

AF:

0.616

AC:

15979

AN:

25959

American (AMR)

AF:

0.684

AC:

24030

AN:

35153

Ashkenazi Jewish (ASJ)

AF:

0.565

AC:

10894

AN:

19270

East Asian (EAS)

AF:

0.839

AC:

25289

AN:

30147

South Asian (SAS)

AF:

0.594

AC:

31895

AN:

53718

European-Finnish (FIN)

AF:

0.541

AC:

21909

AN:

40518

Middle Eastern (MID)

AF:

0.696

AC:

2860

AN:

4108

European-Non Finnish (NFE)

AF:

0.579

AC:

476900

AN:

823453

Other (OTH)

AF:

0.599

AC:

27221

AN:

45432

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.519

Heterozygous variant carriers

10256

20512

30767

41023

51279

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

15088

30176

45264

60352

75440

<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

Data not reliable, filtered out with message: InbreedingCoeff

AF:

0.591

AC:

65239

AN:

110352

Hom.:

13864

Cov.:

AF XY:

0.584

AC XY:

19015

AN XY:

32578

show subpopulations

African (AFR)

AF:

0.605

AC:

18327

AN:

30303

American (AMR)

AF:

0.627

AC:

6540

AN:

10427

Ashkenazi Jewish (ASJ)

AF:

0.558

AC:

1462

AN:

2622

East Asian (EAS)

AF:

0.831

AC:

2900

AN:

3489

South Asian (SAS)

AF:

0.573

AC:

1479

AN:

2582

European-Finnish (FIN)

AF:

0.525

AC:

3048

AN:

5801

Middle Eastern (MID)

AF:

0.705

AC:

146

AN:

207

European-Non Finnish (NFE)

AF:

0.570

AC:

30055

AN:

52734

Other (OTH)

AF:

0.605

AC:

915

AN:

1512

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

977

1954

2932

3909

4886

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

590

1180

1770

2360

2950

<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:

0.588

Hom.:

52303

Bravo

AF:

0.606

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.61

CADD

Benign

4.1

(source)

DANN

Benign

0.45

PhyloP100

0.81

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

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