rs4945851

Positions:

• chr6-110176030-T-C

Variant summary

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

The NM_003931.3(WASF1):​c.-127+2568A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.279 in 151,920 control chromosomes in the GnomAD database, including 8,539 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 0.28 (8539 hom., cov: 32)
• Consequence: WASF1 NM_003931.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.752

Genes affected

WASF1 (HGNC:12732): (WASP family member 1) The protein encoded by this gene, a member of the Wiskott-Aldrich syndrome protein (WASP)-family, plays a critical role downstream of Rac, a Rho-family small GTPase, in regulating the actin cytoskeleton required for membrane ruffling. It has been shown to associate with an actin nucleation core Arp2/3 complex while enhancing actin polymerization in vitro. Wiskott-Aldrich syndrome is a disease of the immune system, likely due to defects in regulation of actin cytoskeleton. Multiple alternatively spliced transcript variants encoding the same protein have been found for this gene. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.568 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
WASF1	NM_003931.3	c.-127+2568A>G		intron_variant		ENST00000392589.6	NP_003922.1
WASF1	NM_001024934.2	c.-29+2568A>G		intron_variant			NP_001020105.1
WASF1	NM_001024935.2	c.-127+3409A>G		intron_variant			NP_001020106.1
WASF1	NM_001024936.2	c.-29+3409A>G		intron_variant			NP_001020107.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
WASF1	ENST00000392589.6	c.-127+2568A>G		intron_variant		5	NM_003931.3	ENSP00000376368	P1

Frequencies

GnomAD3 genomes AF: 0.278 AC: 42253 AN: 151802 Hom.: 8505 Cov.: 32

Gnomad AFR AF: 0.574

Gnomad AMI AF: 0.300

Gnomad AMR AF: 0.204

Gnomad ASJ AF: 0.129

Gnomad EAS AF: 0.222

Gnomad SAS AF: 0.279

Gnomad FIN AF: 0.149

Gnomad MID AF: 0.139

Gnomad NFE AF: 0.149

Gnomad OTH AF: 0.225

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.279 AC: 42354 AN: 151920 Hom.: 8539 Cov.: 32 AF XY: 0.278 AC XY: 20628 AN XY: 74256

Gnomad4 AFR AF: 0.574

Gnomad4 AMR AF: 0.205

Gnomad4 ASJ AF: 0.129

Gnomad4 EAS AF: 0.222

Gnomad4 SAS AF: 0.279

Gnomad4 FIN AF: 0.149

Gnomad4 NFE AF: 0.149

Gnomad4 OTH AF: 0.226

Alfa AF: 0.188 Hom.: 1378

Bravo AF: 0.295

Asia WGS AF: 0.275 AC: 956 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.38
DANN	Benign	0.66

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: rs4945851; hg19: chr6-110497233; COSMIC: COSV55618957; COSMIC: COSV55618957;