chr2-113598759-C-T

Position:

• chr2-113598759-C-T

Variant summary

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

The ENST00000538033.2(WASH2P):​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: WASH2P ENST00000538033.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.116

Genes affected

WASH2P (HGNC:):

ACMG classification

Verdict is Likely_benign. Variant got -4 ACMG points.

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

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
WASH2P	NR_024077.2	n.1681C>T		non_coding_transcript_exon_variant	11/11

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
WASH2P	ENST00000453662.6	n.1409C>T		non_coding_transcript_exon_variant	10/10	6
WASH2P	ENST00000538033.2	n.2516C>T		non_coding_transcript_exon_variant	7/7	2
WASH2P	ENST00000685302.1	n.1777C>T		non_coding_transcript_exon_variant	11/11

Frequencies

GnomAD3 genomes AF: 0.00 AC: 35 AN: 148228 Hom.: 0 Cov.: 33 FAILED QC

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

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

Gnomad4 AFR exome AF: 0.0000979

Gnomad4 AMR exome AF: 0.000316

Gnomad4 ASJ exome AF: 0.000495

Gnomad4 EAS exome AF: 0.0000267

Gnomad4 SAS exome AF: 0.0000761

Gnomad4 FIN exome AF: 0.000307

Gnomad4 NFE exome AF: 0.000195

Gnomad4 OTH exome AF: 0.000355

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

Gnomad4 AFR AF: 0.000243

Gnomad4 AMR AF: 0.0000677

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.000400

Gnomad4 SAS AF: 0.000433

Gnomad4 FIN AF: 0.000396

Gnomad4 NFE AF: 0.000212

Gnomad4 OTH AF: 0.000986

Alfa AF: 0.00488 Hom.: 0

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	7.2
DANN	Benign	0.93

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1045652; hg19: chr2-114356336;