rs7754000

Positions:

• chr6-303017-G-A
• chr6-303017-G-T

Variant summary

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

The NM_001286555.3(DUSP22):​c.22-1611G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0552 in 149,680 control chromosomes in the GnomAD database, including 18 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 0.055 (18 hom., cov: 57)
• Consequence: DUSP22 NM_001286555.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0680

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=-0.83).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0792 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
DUSP22	NM_001286555.3	c.22-1611G>A		intron_variant		ENST00000419235.7	NP_001273484.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
DUSP22	ENST00000419235.7	c.22-1611G>A		intron_variant		2	NM_001286555.3	ENSP00000397459	P1

Frequencies

GnomAD3 genomes AF: 0.0552 AC: 8259 AN: 149562 Hom.: 18 Cov.: 57

Gnomad AFR AF: 0.0129

Gnomad AMI AF: 0.122

Gnomad AMR AF: 0.0525

Gnomad ASJ AF: 0.0667

Gnomad EAS AF: 0.000192

Gnomad SAS AF: 0.00789

Gnomad FIN AF: 0.105

Gnomad MID AF: 0.0288

Gnomad NFE AF: 0.0810

Gnomad OTH AF: 0.0533

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

GnomAD4 genome AF: 0.0552 AC: 8256 AN: 149680 Hom.: 18 Cov.: 57 AF XY: 0.0547 AC XY: 4003 AN XY: 73132

Gnomad4 AFR AF: 0.0128

Gnomad4 AMR AF: 0.0524

Gnomad4 ASJ AF: 0.0667

Gnomad4 EAS AF: 0.000193

Gnomad4 SAS AF: 0.00748

Gnomad4 FIN AF: 0.105

Gnomad4 NFE AF: 0.0810

Gnomad4 OTH AF: 0.0532

Alfa AF: 0.0363 Hom.: 9

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	6.0
DANN	Benign	0.84

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: rs7754000; hg19: chr6-303017;