6-328070-C-G

Position:

• chr6-328070-C-G

Variant summary

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

The NM_001286555.3(DUSP22):​c.139-7044C>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 0.29 (462 hom., cov: 58)
  • Failed GnomAD Quality Control
• Consequence: DUSP22 NM_001286555.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.29

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]

DUSP22 (HGNC:):

ACMG classification

Verdict is Likely_benign. Variant got -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
DUSP22	NM_001286555.3	c.139-7044C>G		intron_variant		ENST00000419235.7	NP_001273484.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
DUSP22	ENST00000419235.7	c.139-7044C>G		intron_variant		2	NM_001286555.3	ENSP00000397459.2

Frequencies

GnomAD3 genomes AF: 0.00 AC: 41158 AN: 142998 Hom.: 462 Cov.: 58 FAILED QC

Gnomad AFR AF: 0.161

Gnomad AMI AF: 0.347

Gnomad AMR AF: 0.320

Gnomad ASJ AF: 0.376

Gnomad EAS AF: 0.177

Gnomad SAS AF: 0.247

Gnomad FIN AF: 0.350

Gnomad MID AF: 0.265

Gnomad NFE AF: 0.356

Gnomad OTH AF: 0.293

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: 0.288 AC: 41166 AN: 143110 Hom.: 462 Cov.: 58 AF XY: 0.285 AC XY: 19905 AN XY: 69902

Gnomad4 AFR AF: 0.160

Gnomad4 AMR AF: 0.320

Gnomad4 ASJ AF: 0.376

Gnomad4 EAS AF: 0.177

Gnomad4 SAS AF: 0.247

Gnomad4 FIN AF: 0.350

Gnomad4 NFE AF: 0.356

Gnomad4 OTH AF: 0.293

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	0.060
DANN	Benign	0.37

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

Publications

LitVar

Other links and lift over

dbSNP: rs11757245; hg19: chr6-328070; COSMIC: COSV60525330;