rs477501

Variant names:

• chr2-113587379-G-C
• rs477501
• ENST00000685302.1:n.293-1171G>C

Your query was ambiguous. Multiple possible variants found:

• chr2-113587379-G-C
• chr2-113587379-G-T

Variant summary

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

The ENST00000685302.1(ENSG00000310523):​n.293-1171G>C variant causes a intron 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: ENSG00000310523 ENST00000685302.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0120
• Publications: 1 publications found

Genes affected

ENSG00000310523 (HGNC:):

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

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

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

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
WASH2P	NR_024077.2	n.277-1171G>C		intron_variant	Intron 1 of 10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000310523	ENST00000685302.1	n.293-1171G>C		intron_variant	Intron 1 of 10
ENSG00000310523	ENST00000685435.1	n.290-1171G>C		intron_variant	Intron 1 of 10
ENSG00000310523	ENST00000685518.1	n.282-1171G>C		intron_variant	Intron 1 of 9

Frequencies

GnomAD3 genomes AF: 0.280 AC: 33229 AN: 118486 Hom.: 0 Cov.: 56

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

⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5.

African (AFR) AF: 0.267 AC: 8339 AN: 31186

American (AMR) AF: 0.296 AC: 3561 AN: 12034

Ashkenazi Jewish (ASJ) AF: 0.302 AC: 843 AN: 2788

East Asian (EAS) AF: 0.363 AC: 1487 AN: 4094

South Asian (SAS) AF: 0.282 AC: 1079 AN: 3830

European-Finnish (FIN) AF: 0.281 AC: 2373 AN: 8438

Middle Eastern (MID) AF: 0.319 AC: 76 AN: 238

European-Non Finnish (NFE) AF: 0.275 AC: 14730 AN: 53548

Other (OTH) AF: 0.284 AC: 470 AN: 1656

⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5. (p-value = 0), which strongly suggests a high chance of mosaicism in these individuals.

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
PhyloP100		-0.012

Splicing

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

Other links and lift over

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