dbSNP rs2853930: WASF5P:n.1318T>G (chr6-31287647-A-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.1318T>G variant causes a non coding transcript exon change. The variant allele was found at a frequency of 0.103 in 152,842 control chromosomes in the GnomAD database, including 901 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 ( 898 hom., cov: 32)

Exomes 𝑓: 0.10 ( 3 hom. )

Consequence

WASF5P
ENST00000428639.1 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 6.05

Publications

8 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:

Genome browser will be placed here

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=-0.58).

BA1

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

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
WASF5P		n.31287647A>C		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
WASF5P	ENST00000428639.1 link	n.1318T>G		non_coding_transcript_exon_variant	Exon 1 of 1	6
ENSG00000298396	ENST00000755297.1 link	n.32+16541A>C		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes

AF:

0.103

AC:

15682

AN:

152098

Hom.:

899

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0764

Gnomad AMI

AF:

0.127

Gnomad AMR

AF:

0.115

Gnomad ASJ

AF:

0.150

Gnomad EAS

AF:

0.103

Gnomad SAS

AF:

0.0712

Gnomad FIN

AF:

0.0522

Gnomad MID

AF:

0.0538

Gnomad NFE

AF:

0.124

Gnomad OTH

AF:

0.115

GnomAD4 exome

AF:

0.102

AC:

AN:

626

Hom.:

Cov.:

AF XY:

0.0925

AC XY:

AN XY:

400

show subpopulations

African (AFR)

AF:

0.00

AC:

AN:

American (AMR)

AF:

0.0833

AC:

AN:

Ashkenazi Jewish (ASJ)

AF:

0.500

AC:

AN:

East Asian (EAS)

AF:

0.0833

AC:

AN:

South Asian (SAS)

AF:

0.300

AC:

AN:

European-Finnish (FIN)

AF:

0.0614

AC:

AN:

114

Middle Eastern (MID)

AF:

0.0469

AC:

AN:

European-Non Finnish (NFE)

AF:

0.102

AC:

AN:

294

Other (OTH)

AF:

0.154

AC:

AN:

104

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.566

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:

0.103

AC:

15678

AN:

152216

Hom.:

898

Cov.:

AF XY:

0.0977

AC XY:

7275

AN XY:

74440

show subpopulations

African (AFR)

AF:

0.0762

AC:

3165

AN:

41528

American (AMR)

AF:

0.115

AC:

1753

AN:

15294

Ashkenazi Jewish (ASJ)

AF:

0.150

AC:

522

AN:

3472

East Asian (EAS)

AF:

0.103

AC:

532

AN:

5176

South Asian (SAS)

AF:

0.0708

AC:

342

AN:

4830

European-Finnish (FIN)

AF:

0.0522

AC:

554

AN:

10608

Middle Eastern (MID)

AF:

0.0476

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.124

AC:

8438

AN:

67992

Other (OTH)

AF:

0.115

AC:

242

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

751

1501

2252

3002

3753

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

162

324

486

648

810

<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:

0.118

Hom.:

1028

Bravo

AF:

0.108

Asia WGS

AF:

0.0870

AC:

303

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.58

CADD

Benign

(source)

DANN

Benign

0.57

PhyloP100

6.1

Splicing

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

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over