6-328070-C-G

Variant names:

• chr6-328070-C-G
• rs11757245
• NM_001286555.3:c.139-7044C>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.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
• Publications: 3 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=-0.82).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001286555.3. 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
	DUSP22	NM_001286555.3	MANE Select	c.139-7044C>G		intron	N/A	NP_001273484.1	Q9NRW4-2
	DUSP22	NM_020185.6		c.139-7044C>G		intron	N/A	NP_064570.1	Q9NRW4-1
	DUSP22	NR_104473.3		n.191+16108C>G		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DUSP22	ENST00000419235.7	TSL:2 MANE Select	c.139-7044C>G		intron	N/A	ENSP00000397459.2	Q9NRW4-2
	DUSP22	ENST00000344450.9	TSL:1	c.139-7044C>G		intron	N/A	ENSP00000345281.5	Q9NRW4-1
	DUSP22	ENST00000603453.5	TSL:4	c.-171-7044C>G		intron	N/A	ENSP00000474646.1	S4R3M1

Frequencies

GnomAD3 genomes AF: 0.288 AC: 41158 AN: 142998 Hom.: 462 Cov.: 58

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

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

African (AFR) AF: 0.160 AC: 6340 AN: 39506

American (AMR) AF: 0.320 AC: 4570 AN: 14302

Ashkenazi Jewish (ASJ) AF: 0.376 AC: 1247 AN: 3314

East Asian (EAS) AF: 0.177 AC: 883 AN: 4994

South Asian (SAS) AF: 0.247 AC: 1115 AN: 4510

European-Finnish (FIN) AF: 0.350 AC: 3422 AN: 9768

Middle Eastern (MID) AF: 0.257 AC: 72 AN: 280

European-Non Finnish (NFE) AF: 0.356 AC: 22642 AN: 63604

Other (OTH) AF: 0.293 AC: 577 AN: 1972

⚠️ 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: 0.00 Hom.: 0

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	0.060
DANN	Benign	0.37
PhyloP100		-2.3
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: rs11757245; hg19: chr6-328070; COSMIC: COSV60525330;