X-156025065-C-A

Variant names:

• chrX-156025065-C-A
• rs772298164
• ENST00000359512.8:c.1268C>A

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2

The ENST00000359512.8(WASH6P):​c.1268C>A​(p.Ser423*) variant causes a stop gained change. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 40)
  • Exomes 𝑓: 7.1e-7 (0 hom. 1 hem.)
  • Failed GnomAD Quality Control
• Consequence: WASH6P ENST00000359512.8 stop_gained
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 5.26

Genes affected

WASH6P (HGNC:31685): (WASP family homolog 6, pseudogene) Predicted to enable alpha-tubulin binding activity. Predicted to be involved in Arp2/3 complex-mediated actin nucleation and retrograde transport, endosome to Golgi. Predicted to be located in early endosome and recycling endosome. Predicted to be part of WASH complex. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Uncertain_significance. Variant got 2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
WASH6P		n.156025065C>A		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
WASH6P	ENST00000359512.8	c.1268C>A	p.Ser423*	stop_gained	Exon 9 of 10	6		ENSP00000504557.1

Frequencies

GnomAD3 genomes Cov.: 40

GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 7.15e-7 AC: 1 AN: 1399530 Hom.: 0 Cov.: 32 AF XY: 0.00000145 AC XY: 1 AN XY: 691456

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 9.29e-7

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome Cov.: 40

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.45
CADD	Pathogenic	34
DANN	Benign	0.96
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.0

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs772298164; hg19: chrX-155254730;