rs2853930

Positions:

• chr6-31287647-A-C
• chr6-31287647-A-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 6.05

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]

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
WASF5P	ENST00000428639.1	n.1318T>G		non_coding_transcript_exon_variant	1/1

Frequencies

GnomAD3 genomes AF: 0.103 AC: 15682 AN: 152098 Hom.: 899 Cov.: 32

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: 64 AN: 626 Hom.: 3 Cov.: 0 AF XY: 0.0925 AC XY: 37 AN XY: 400

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.0833

Gnomad4 ASJ exome AF: 0.500

Gnomad4 EAS exome AF: 0.0833

Gnomad4 SAS exome AF: 0.300

Gnomad4 FIN exome AF: 0.0614

Gnomad4 NFE exome AF: 0.102

Gnomad4 OTH exome AF: 0.154

GnomAD4 genome AF: 0.103 AC: 15678 AN: 152216 Hom.: 898 Cov.: 32 AF XY: 0.0977 AC XY: 7275 AN XY: 74440

Gnomad4 AFR AF: 0.0762

Gnomad4 AMR AF: 0.115

Gnomad4 ASJ AF: 0.150

Gnomad4 EAS AF: 0.103

Gnomad4 SAS AF: 0.0708

Gnomad4 FIN AF: 0.0522

Gnomad4 NFE AF: 0.124

Gnomad4 OTH AF: 0.115

Alfa AF: 0.119 Hom.: 719

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	12
DANN	Benign	0.57

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2853930; hg19: chr6-31255424;