X-47803573-T-G

Variant names:

• chrX-47803573-T-G
• rs909713
• ENST00000444248.1:n.278T>G

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_Strong

The ENST00000811713.1(ENSG00000305567):​n.446A>C 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: ENSG00000305567 ENST00000811713.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.813
• Publications: 10 publications found

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]

ENSG00000305567 (HGNC:):

ACMG classification

Our verdict: Likely_benign. The variant received -4 ACMG points.

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

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000811713.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	WASF4P	ENST00000444248.1	TSL:6	n.278T>G		non_coding_transcript_exon	Exon 1 of 1
	ENSG00000305567	ENST00000811713.1		n.446A>C		non_coding_transcript_exon	Exon 4 of 4
	ENSG00000305567	ENST00000811714.1		n.481A>C		non_coding_transcript_exon	Exon 4 of 4

Frequencies

GnomAD3 genomes AF: 0.591 AC: 65202 AN: 110302 Hom.: 13864 Cov.: 23

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

GnomAD2 exomes AF: 0.611 AC: 111764 AN: 183001 AF XY: 0.607

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 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

African (AFR) AF: 0.616 AC: 15979 AN: 25959

American (AMR) AF: 0.684 AC: 24030 AN: 35153

Ashkenazi Jewish (ASJ) AF: 0.565 AC: 10894 AN: 19270

East Asian (EAS) AF: 0.839 AC: 25289 AN: 30147

South Asian (SAS) AF: 0.594 AC: 31895 AN: 53718

European-Finnish (FIN) AF: 0.541 AC: 21909 AN: 40518

Middle Eastern (MID) AF: 0.696 AC: 2860 AN: 4108

European-Non Finnish (NFE) AF: 0.579 AC: 476900 AN: 823453

Other (OTH) AF: 0.599 AC: 27221 AN: 45432

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

African (AFR) AF: 0.605 AC: 18327 AN: 30303

American (AMR) AF: 0.627 AC: 6540 AN: 10427

Ashkenazi Jewish (ASJ) AF: 0.558 AC: 1462 AN: 2622

East Asian (EAS) AF: 0.831 AC: 2900 AN: 3489

South Asian (SAS) AF: 0.573 AC: 1479 AN: 2582

European-Finnish (FIN) AF: 0.525 AC: 3048 AN: 5801

Middle Eastern (MID) AF: 0.705 AC: 146 AN: 207

European-Non Finnish (NFE) AF: 0.570 AC: 30055 AN: 52734

Other (OTH) AF: 0.605 AC: 915 AN: 1512

Alfa AF: 0.588 Hom.: 52303

Bravo AF: 0.606

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.61
CADD	Benign	4.1
DANN	Benign	0.45
PhyloP100		0.81

Splicing

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

Other links and lift over

dbSNP: rs909713; hg19: chrX-47662972;