6-349386-T-G

Variant names:

• chr6-349386-T-G
• rs7763092
• NM_001286555.3:c.*435T>G

Variant summary

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

The NM_001286555.3(DUSP22):​c.*435T>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0162 in 1,019,138 control chromosomes in the GnomAD database, including 7 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 0.029 (2 hom., cov: 59)
  • Exomes 𝑓: 0.014 (5 hom.)
• Consequence: DUSP22 NM_001286555.3 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0910

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=-0.8).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0732 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DUSP22	NM_001286555.3	c.*435T>G		3_prime_UTR_variant	Exon 7 of 7	ENST00000419235.7	NP_001273484.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DUSP22	ENST00000419235.7	c.*435T>G		3_prime_UTR_variant	Exon 7 of 7	2	NM_001286555.3	ENSP00000397459.2

Frequencies

GnomAD3 genomes AF: 0.0284 AC: 4288 AN: 150872 Hom.: 2 Cov.: 59

Gnomad AFR AF: 0.0749

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0200

Gnomad ASJ AF: 0.0208

Gnomad EAS AF: 0.000192

Gnomad SAS AF: 0.00289

Gnomad FIN AF: 0.00179

Gnomad MID AF: 0.0158

Gnomad NFE AF: 0.0118

Gnomad OTH AF: 0.0226

GnomAD4 exome AF: 0.0140 AC: 12192 AN: 868148 Hom.: 5 Cov.: 98 AF XY: 0.0139 AC XY: 5605 AN XY: 403488

Gnomad4 AFR exome AF: 0.0801

Gnomad4 AMR exome AF: 0.0110

Gnomad4 ASJ exome AF: 0.0233

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00307

Gnomad4 FIN exome AF: 0.00249

Gnomad4 NFE exome AF: 0.0130

Gnomad4 OTH exome AF: 0.0148

GnomAD4 genome AF: 0.0286 AC: 4317 AN: 150990 Hom.: 2 Cov.: 59 AF XY: 0.0281 AC XY: 2078 AN XY: 73888

Gnomad4 AFR AF: 0.0754

Gnomad4 AMR AF: 0.0199

Gnomad4 ASJ AF: 0.0208

Gnomad4 EAS AF: 0.000193

Gnomad4 SAS AF: 0.00269

Gnomad4 FIN AF: 0.00179

Gnomad4 NFE AF: 0.0118

Gnomad4 OTH AF: 0.0223

Alfa AF: 0.0271 Hom.: 7

Asia WGS AF: 0.0110 AC: 38 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	0.73
DANN	Benign	0.67

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: rs7763092; hg19: chr6-349386;