16-16628-G-A

Variant names:

• chr16-16628-G-A
• rs373734467
• ENST00000564273.4:n.643C>T

Variant summary

Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_Strong BP6_Moderate

The ENST00000564273.4(WASH4P):​n.643C>T 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. Variant has been reported in ClinVar as Likely benign (★).

• Frequency:
  • Genomes: 𝑓 0.00022 (0 hom., cov: 16)
  • Exomes 𝑓: 0.000098 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: WASH4P ENST00000564273.4 non_coding_transcript_exon
• Clinical Significance: Likely benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.406

Genes affected

WASH4P (HGNC:14126): (WASP family homolog 4, 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 Likely_benign. Variant got -6 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.6).
• BP6: Variant 16-16628-G-A is Benign according to our data. Variant chr16-16628-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 3771411.Status of the report is criteria_provided_single_submitter, 1 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
WASH4P		n.16628G>A		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
WASH4P	ENST00000564273.4	n.643C>T		non_coding_transcript_exon_variant	Exon 5 of 9	6

Frequencies

GnomAD3 genomes AF: 0.000220 AC: 28 AN: 127418 Hom.: 0 Cov.: 16

Gnomad AFR AF: 0.000369

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00204

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.000115

Gnomad OTH AF: 0.00

GnomAD3 exomes AF: 0.000149 AC: 9 AN: 60606 Hom.: 0 AF XY: 0.000194 AC XY: 6 AN XY: 30910

Gnomad AFR exome AF: 0.000216

Gnomad AMR exome AF: 0.0000748

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.000571

Gnomad SAS exome AF: 0.00

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.0000927

Gnomad OTH exome AF: 0.00

GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.0000981 AC: 48 AN: 489246 Hom.: 0 Cov.: 4 AF XY: 0.0000886 AC XY: 23 AN XY: 259512

Gnomad4 AFR exome AF: 0.000447

Gnomad4 AMR exome AF: 0.0000337

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.000320

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.0000657

Gnomad4 NFE exome AF: 0.0000835

Gnomad4 OTH exome AF: 0.000145

GnomAD4 genome AF: 0.000220 AC: 28 AN: 127516 Hom.: 0 Cov.: 16 AF XY: 0.000278 AC XY: 17 AN XY: 61204

Gnomad4 AFR AF: 0.000367

Gnomad4 AMR AF: 0.00

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00204

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.000115

Gnomad4 OTH AF: 0.00

Alfa AF: 0.0000843 Hom.: 0

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Jan 01, 2025

CeGaT Center for Human Genetics Tuebingen

Significance: Likely benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

WASH4P: BP4, BP7 -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.60
CADD	Benign	0.0090
DANN	Benign	0.81

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs373734467; hg19: chr16-66628;