2-113598759-C-T

Variant names:

• chr2-113598759-C-T
• rs1045652
• ENST00000453662.6:n.1409C>T

Variant summary

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

The ENST00000538033.2(ENSG00000310523):​n.2516C>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. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.00024 (0 hom., cov: 33)
  • Exomes 𝑓: 0.00020 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: ENSG00000310523 ENST00000538033.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.116
• Publications: 1 publications found

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]

ENSG00000310523 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000538033.2. 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
	WASH2P	NR_024077.2		n.1681C>T		non_coding_transcript_exon	Exon 11 of 11

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	WASH2P	ENST00000453662.6	TSL:6	n.1409C>T		non_coding_transcript_exon	Exon 10 of 10
	ENSG00000310523	ENST00000538033.2	TSL:2	n.2516C>T		non_coding_transcript_exon	Exon 7 of 7
	ENSG00000310523	ENST00000685302.1		n.1777C>T		non_coding_transcript_exon	Exon 11 of 11

Frequencies

GnomAD3 genomes AF: 0.000236 AC: 35 AN: 148228 Hom.: 0 Cov.: 33

Gnomad AFR AF: 0.000244

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0000678

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.000399

Gnomad SAS AF: 0.000432

Gnomad FIN AF: 0.000396

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.000212

Gnomad OTH AF: 0.000991

GnomAD2 exomes AF: 0.000423 AC: 83 AN: 196362 AF XY: 0.000478

Gnomad AFR exome AF: 0.00

Gnomad AMR exome AF: 0.000463

Gnomad ASJ exome AF: 0.000271

Gnomad EAS exome AF: 0.000185

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.000570

Gnomad OTH exome AF: 0.000610

GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.000203 AC: 258 AN: 1270322 Hom.: 0 Cov.: 31 AF XY: 0.000202 AC XY: 128 AN XY: 635072

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

African (AFR) AF: 0.0000979 AC: 3 AN: 30630

American (AMR) AF: 0.000316 AC: 13 AN: 41098

Ashkenazi Jewish (ASJ) AF: 0.000495 AC: 11 AN: 22224

East Asian (EAS) AF: 0.0000267 AC: 1 AN: 37494

South Asian (SAS) AF: 0.0000761 AC: 6 AN: 78808

European-Finnish (FIN) AF: 0.000307 AC: 15 AN: 48832

Middle Eastern (MID) AF: 0.00110 AC: 4 AN: 3624

European-Non Finnish (NFE) AF: 0.000195 AC: 186 AN: 954094

Other (OTH) AF: 0.000355 AC: 19 AN: 53518

⚠️ The allele balance in gnomAD4 Exomes is highly skewed from 0.5 (p-value = 0), which strongly suggests a high chance of mosaicism in these individuals.

GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR AF: 0.000236 AC: 35 AN: 148326 Hom.: 0 Cov.: 33 AF XY: 0.000235 AC XY: 17 AN XY: 72352

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

African (AFR) AF: 0.000243 AC: 10 AN: 41102

American (AMR) AF: 0.0000677 AC: 1 AN: 14774

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3394

East Asian (EAS) AF: 0.000400 AC: 2 AN: 4998

South Asian (SAS) AF: 0.000433 AC: 2 AN: 4622

European-Finnish (FIN) AF: 0.000396 AC: 4 AN: 10104

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 274

European-Non Finnish (NFE) AF: 0.000212 AC: 14 AN: 66142

Other (OTH) AF: 0.000986 AC: 2 AN: 2028

⚠️ 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: 0.00488 Hom.: 0

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	7.2
DANN	Benign	0.93
PhyloP100		0.12
Mutation Taster		=100/0	polymorphism

Splicing

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

Other links and lift over

dbSNP: rs1045652; hg19: chr2-114356336;