rs12198312

chr6-323326-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001286555.3(DUSP22):c.138+11364C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0834 in 148,832 control chromosomes in the GnomAD database, including 39 homozygotes. 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 0.083 (39 hom., cov: 60)
• Consequence: DUSP22 NM_001286555.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.330

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.77).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.111 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
DUSP22	NM_001286555.3	c.138+11364C>T		intron_variant		ENST00000419235.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
DUSP22	ENST00000419235.7	c.138+11364C>T		intron_variant		2	NM_001286555.3	P1

Frequencies

GnomAD3 genomes AF: 0.0833 AC: 12383 AN: 148716 Hom.: 39 Cov.: 60

Gnomad AFR AF: 0.0528

Gnomad AMI AF: 0.0886

Gnomad AMR AF: 0.0735

Gnomad ASJ AF: 0.0777

Gnomad EAS AF: 0.000961

Gnomad SAS AF: 0.0166

Gnomad FIN AF: 0.104

Gnomad MID AF: 0.0728

Gnomad NFE AF: 0.113

Gnomad OTH AF: 0.0786

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.0834 AC: 12406 AN: 148832 Hom.: 39 Cov.: 60 AF XY: 0.0812 AC XY: 5909 AN XY: 72774

Gnomad4 AFR AF: 0.0529

Gnomad4 AMR AF: 0.0735

Gnomad4 ASJ AF: 0.0777

Gnomad4 EAS AF: 0.000963

Gnomad4 SAS AF: 0.0166

Gnomad4 FIN AF: 0.104

Gnomad4 NFE AF: 0.113

Gnomad4 OTH AF: 0.0826

Alfa AF: 0.0986 Hom.: 46

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
Cadd	Benign	7.6
Dann	Benign	0.81

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: rs12198312; hg19: chr6-323326;