rs11548323

chr1-27405147-C-T

Variant summary

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

The NM_006990.5(WASF2):c.*3042G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.143 in 152,240 control chromosomes in the GnomAD database, including 1,679 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 0.14 (1676 hom., cov: 32)
  • Exomes 𝑓: 0.24 (3 hom.)
• Consequence: WASF2 NM_006990.5 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.929

Genes affected

WASF2 (HGNC:12733): (WASP family member 2) This gene encodes a member of the Wiskott-Aldrich syndrome protein family. The gene product is a protein that forms a multiprotein complex that links receptor kinases and actin. Binding to actin occurs through a C-terminal verprolin homology domain in all family members. The multiprotein complex serves to tranduce signals that involve changes in cell shape, motility or function. The published map location (PMID:10381382) has been changed based on recent genomic sequence comparisons, which indicate that the expressed gene is located on chromosome 1, and a pseudogene may be located on chromosome X. Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jan 2011]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.48).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.17 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
WASF2	NM_006990.5	c.*3042G>A		3_prime_UTR_variant	9/9	ENST00000618852.5
WASF2	NM_001201404.3	c.*3178G>A		3_prime_UTR_variant	8/8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
WASF2	ENST00000618852.5	c.*3042G>A		3_prime_UTR_variant	9/9	1	NM_006990.5	P1

Frequencies

GnomAD3 genomes AF: 0.143 AC: 21723 AN: 152060 Hom.: 1673 Cov.: 32

Gnomad AFR AF: 0.127

Gnomad AMI AF: 0.292

Gnomad AMR AF: 0.107

Gnomad ASJ AF: 0.0890

Gnomad EAS AF: 0.0621

Gnomad SAS AF: 0.0747

Gnomad FIN AF: 0.142

Gnomad MID AF: 0.165

Gnomad NFE AF: 0.172

Gnomad OTH AF: 0.141

GnomAD4 exome AF: 0.242 AC: 15 AN: 62 Hom.: 3 Cov.: 0 AF XY: 0.250 AC XY: 10 AN XY: 40

Gnomad4 FIN exome AF: 0.167

Gnomad4 NFE exome AF: 0.300

Gnomad4 OTH exome AF: 0.100

GnomAD4 genome AF: 0.143 AC: 21730 AN: 152178 Hom.: 1676 Cov.: 32 AF XY: 0.140 AC XY: 10442 AN XY: 74416

Gnomad4 AFR AF: 0.127

Gnomad4 AMR AF: 0.107

Gnomad4 ASJ AF: 0.0890

Gnomad4 EAS AF: 0.0614

Gnomad4 SAS AF: 0.0743

Gnomad4 FIN AF: 0.142

Gnomad4 NFE AF: 0.172

Gnomad4 OTH AF: 0.142

Alfa AF: 0.159 Hom.: 2791

Bravo AF: 0.140

Asia WGS AF: 0.0950 AC: 330 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.48
Cadd	Benign	19
Dann	Benign	0.92
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs11548323; hg19: chr1-27731651;