X-47803573-T-G

Position:

• chrX-47803573-T-G

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong

The ENST00000444248.1(WASF4P):​n.278T>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. 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 0.59 (13864 hom., 19015 hem., cov: 23)
  • Exomes 𝑓: 0.59 (126816 hom. 209530 hem.)
  • Failed GnomAD Quality Control
• Consequence: WASF4P ENST00000444248.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.813

Genes affected

WASF4P (HGNC:20801): (WASP family member 4, 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, most closely resembles the gene encoding the WAS protein family member 2, which is located on chromosome 1. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Likely_benign. Variant got -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.61).

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
WASF4P	ENST00000444248.1	n.278T>G		non_coding_transcript_exon_variant	1/1

Frequencies

GnomAD3 genomes AF: 0.591 AC: 65202 AN: 110302 Hom.: 13864 Cov.: 23 AF XY: 0.583 AC XY: 18971 AN XY: 32518

Gnomad AFR AF: 0.605

Gnomad AMI AF: 0.544

Gnomad AMR AF: 0.627

Gnomad ASJ AF: 0.558

Gnomad EAS AF: 0.831

Gnomad SAS AF: 0.572

Gnomad FIN AF: 0.525

Gnomad MID AF: 0.706

Gnomad NFE AF: 0.570

Gnomad OTH AF: 0.602

GnomAD3 exomes AF: 0.611 AC: 111764 AN: 183001 Hom.: 22089 AF XY: 0.607 AC XY: 40918 AN XY: 67461

Gnomad AFR exome AF: 0.613

Gnomad AMR exome AF: 0.688

Gnomad ASJ exome AF: 0.572

Gnomad EAS exome AF: 0.835

Gnomad SAS exome AF: 0.583

Gnomad FIN exome AF: 0.542

Gnomad NFE exome AF: 0.571

Gnomad OTH exome AF: 0.595

GnomAD4 exome Data not reliable, filtered out with message: InbreedingCoeff AF: 0.591 AC: 636977 AN: 1077758 Hom.: 126816 Cov.: 34 AF XY: 0.595 AC XY: 209530 AN XY: 351988

Gnomad4 AFR exome AF: 0.616

Gnomad4 AMR exome AF: 0.684

Gnomad4 ASJ exome AF: 0.565

Gnomad4 EAS exome AF: 0.839

Gnomad4 SAS exome AF: 0.594

Gnomad4 FIN exome AF: 0.541

Gnomad4 NFE exome AF: 0.579

Gnomad4 OTH exome AF: 0.599

GnomAD4 genome Data not reliable, filtered out with message: InbreedingCoeff AF: 0.591 AC: 65239 AN: 110352 Hom.: 13864 Cov.: 23 AF XY: 0.584 AC XY: 19015 AN XY: 32578

Gnomad4 AFR AF: 0.605

Gnomad4 AMR AF: 0.627

Gnomad4 ASJ AF: 0.558

Gnomad4 EAS AF: 0.831

Gnomad4 SAS AF: 0.573

Gnomad4 FIN AF: 0.525

Gnomad4 NFE AF: 0.570

Gnomad4 OTH AF: 0.605

Alfa AF: 0.583 Hom.: 35364

Bravo AF: 0.606

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.61
CADD	Benign	4.1
DANN	Benign	0.45

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs909713; hg19: chrX-47662972;