Genetic Variant ENST00000428639.1: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:

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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.

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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	WASF5P	ENST00000428639.1	TSL:6	n.1318T>G		non_coding_transcript_exon	Exon 1 of 1
	ENSG00000298396	ENST00000755297.1		n.32+16541A>C		intron	N/A

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 v4.9

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

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over