rs815593

Variant names:

• chr6-294457-A-G
• rs815593
• NM_001286555.3:c.21+1897A>G

Variant summary

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

The NM_001286555.3(DUSP22):​c.21+1897A>G 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 0.44 (5105 hom., cov: 51)
  • Failed GnomAD Quality Control
• Consequence: DUSP22 NM_001286555.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.942
• Publications: 2 publications found

Genes affected

DUSP22 (HGNC:16077): (dual specificity phosphatase 22) Enables non-membrane spanning protein tyrosine phosphatase activity and protein tyrosine kinase binding activity. Involved in several processes, including cellular response to epidermal growth factor stimulus; negative regulation of focal adhesion assembly; and negative regulation of non-membrane spanning protein tyrosine kinase activity. Acts upstream of or within negative regulation of transcription by RNA polymerase II. Located in plasma membrane. Part of cytoplasm; filamentous actin; and leading edge of lamellipodium. [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=-0.91).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DUSP22	NM_001286555.3	c.21+1897A>G		intron_variant	Intron 1 of 6	ENST00000419235.7	NP_001273484.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DUSP22	ENST00000419235.7	c.21+1897A>G		intron_variant	Intron 1 of 6	2	NM_001286555.3	ENSP00000397459.2

Frequencies

GnomAD3 genomes AF: 0.441 AC: 64581 AN: 146296 Hom.: 5103 Cov.: 51

Gnomad AFR AF: 0.397

Gnomad AMI AF: 0.486

Gnomad AMR AF: 0.409

Gnomad ASJ AF: 0.541

Gnomad EAS AF: 0.160

Gnomad SAS AF: 0.294

Gnomad FIN AF: 0.452

Gnomad MID AF: 0.472

Gnomad NFE AF: 0.499

Gnomad OTH AF: 0.453

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: 0.441 AC: 64618 AN: 146404 Hom.: 5105 Cov.: 51 AF XY: 0.434 AC XY: 31071 AN XY: 71588

African (AFR) AF: 0.397 AC: 15402 AN: 38830

American (AMR) AF: 0.409 AC: 6057 AN: 14808

Ashkenazi Jewish (ASJ) AF: 0.541 AC: 1835 AN: 3394

East Asian (EAS) AF: 0.160 AC: 813 AN: 5082

South Asian (SAS) AF: 0.295 AC: 1345 AN: 4566

European-Finnish (FIN) AF: 0.452 AC: 4570 AN: 10104

Middle Eastern (MID) AF: 0.473 AC: 139 AN: 294

European-Non Finnish (NFE) AF: 0.499 AC: 33116 AN: 66408

Other (OTH) AF: 0.448 AC: 911 AN: 2034

Alfa AF: 0.469 Hom.: 718

Asia WGS AF: 0.223 AC: 776 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.33
DANN	Benign	0.28
PhyloP100		-0.94
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs815593; hg19: chr6-294457;