Genetic Variant WASF5P:n.1201A>G (chr6-31287764-T-C) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000428639.1(WASF5P):n.1201A>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.104 in 152,796 control chromosomes in the GnomAD database, including 915 homozygotes. 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 0.10 ( 905 hom., cov: 31)

Exomes 𝑓: 0.12 ( 10 hom. )

Consequence

WASF5P
ENST00000428639.1 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.482

Publications

18 publications found

Variant links:

Genes affected

WASF5P (HGNC:21665): (WASP family member 5, 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, resembles the gene encoding the WAS protein family member 3, which is located on chromosome 13. [provided by RefSeq, Jul 2008]

WASF5P links:

ENSG00000298396 (HGNC:):

ENSG00000298396 links:

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new If you want to explore the variant's impact on the transcript ENST00000428639.1, 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: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.93).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.122 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000428639.1. 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	WASF5P	ENST00000428639.1	TSL:6	n.1201A>G		non_coding_transcript_exon	Exon 1 of 1
	ENSG00000298396	ENST00000755297.1		n.32+16658T>C		intron	N/A

Frequencies

GnomAD3 genomes

AF:

0.104

AC:

15689

AN:

150754

Hom.:

906

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0783

Gnomad AMI

AF:

0.127

Gnomad AMR

AF:

0.116

Gnomad ASJ

AF:

0.150

Gnomad EAS

AF:

0.103

Gnomad SAS

AF:

0.0707

Gnomad FIN

AF:

0.0526

Gnomad MID

AF:

0.0541

Gnomad NFE

AF:

0.124

Gnomad OTH

AF:

0.116

GnomAD4 exome

AF:

0.119

AC:

229

AN:

1926

Hom.:

Cov.:

AF XY:

0.114

AC XY:

130

AN XY:

1142

show subpopulations

African (AFR)

AF:

0.100

AC:

AN:

American (AMR)

AF:

0.167

AC:

AN:

Ashkenazi Jewish (ASJ)

AF:

0.167

AC:

AN:

East Asian (EAS)

AF:

0.0588

AC:

AN:

South Asian (SAS)

AF:

0.0862

AC:

AN:

European-Finnish (FIN)

AF:

0.0714

AC:

AN:

266

Middle Eastern (MID)

AF:

0.0419

AC:

AN:

406

European-Non Finnish (NFE)

AF:

0.172

AC:

145

AN:

842

Other (OTH)

AF:

0.123

AC:

AN:

236

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.547

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

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:

0.104

AC:

15686

AN:

150870

Hom.:

905

Cov.:

AF XY:

0.0987

AC XY:

7277

AN XY:

73740

show subpopulations

African (AFR)

AF:

0.0782

AC:

3176

AN:

40626

American (AMR)

AF:

0.116

AC:

1747

AN:

15090

Ashkenazi Jewish (ASJ)

AF:

0.150

AC:

522

AN:

3470

East Asian (EAS)

AF:

0.103

AC:

533

AN:

5180

South Asian (SAS)

AF:

0.0704

AC:

337

AN:

4788

European-Finnish (FIN)

AF:

0.0526

AC:

557

AN:

10580

Middle Eastern (MID)

AF:

0.0479

AC:

AN:

292

European-Non Finnish (NFE)

AF:

0.124

AC:

8443

AN:

67838

Other (OTH)

AF:

0.115

AC:

241

AN:

2096

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.506

Heterozygous variant carriers

725

1449

2174

2898

3623

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

164

328

492

656

820

<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:

0.114

Hom.:

3523

Bravo

AF:

0.108

Asia WGS

AF:

0.0870

AC:

303

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.93

CADD

Benign

(source)

DANN

Benign

0.67

PhyloP100

0.48

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