2-113587379-G-C

Position:

• chr2-113587379-G-C

Variant summary

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

The NR_024077.2(WASH2P):​n.277-1171G>C variant causes a intron, non coding transcript 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 0.28 (0 hom., cov: 56)
  • Failed GnomAD Quality Control
• Consequence: WASH2P NR_024077.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0120

Genes affected

WASH2P (HGNC:33145): (WASP family homolog 2, 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 -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.07).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
WASH2P	NR_024077.2	n.277-1171G>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
WASH2P	ENST00000686495.1	n.31-1171G>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.00 AC: 33229 AN: 118486 Hom.: 0 Cov.: 56 FAILED QC

Gnomad AFR AF: 0.268

Gnomad AMI AF: 0.379

Gnomad AMR AF: 0.296

Gnomad ASJ AF: 0.302

Gnomad EAS AF: 0.363

Gnomad SAS AF: 0.281

Gnomad FIN AF: 0.281

Gnomad MID AF: 0.313

Gnomad NFE AF: 0.275

Gnomad OTH AF: 0.287

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

GnomAD4 genome Data not reliable, filtered out with message: InbreedingCoeff AF: 0.280 AC: 33248 AN: 118578 Hom.: 0 Cov.: 56 AF XY: 0.281 AC XY: 16255 AN XY: 57948

Gnomad4 AFR AF: 0.267

Gnomad4 AMR AF: 0.296

Gnomad4 ASJ AF: 0.302

Gnomad4 EAS AF: 0.363

Gnomad4 SAS AF: 0.282

Gnomad4 FIN AF: 0.281

Gnomad4 NFE AF: 0.275

Gnomad4 OTH AF: 0.284

Alfa AF: 0.129 Hom.: 0

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	17
DANN	Benign	0.75

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs477501; hg19: chr2-114344956; COSMIC: COSV58541420;