rs7763092

Variant names:

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

Your query was ambiguous. Multiple possible variants found:

• chr6-349386-T-C
• chr6-349386-T-G

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_001286555.3(DUSP22):​c.*435T>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000115 in 871,522 control chromosomes in the GnomAD database, with no homozygous occurrence. 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: not found (cov: 59)
  • Exomes 𝑓: 0.0000011 (0 hom.)
• Consequence: DUSP22 NM_001286555.3 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0910
• Publications: 0 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 -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).

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.*435T>C		3_prime_UTR	Exon 7 of 7	NP_001273484.1	Q9NRW4-2
	DUSP22	NM_020185.6		c.508+545T>C		intron	N/A	NP_064570.1	Q9NRW4-1
	DUSP22	NR_104473.3		n.1056T>C		non_coding_transcript_exon	Exon 6 of 6

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DUSP22	ENST00000419235.7	TSL:2 MANE Select	c.*435T>C		3_prime_UTR	Exon 7 of 7	ENSP00000397459.2	Q9NRW4-2
	DUSP22	ENST00000344450.9	TSL:1	c.508+545T>C		intron	N/A	ENSP00000345281.5	Q9NRW4-1
	DUSP22	ENST00000604971.5	TSL:2	c.*435T>C		3_prime_UTR	Exon 4 of 4	ENSP00000474505.1	S4R3M1

Frequencies

GnomAD3 genomes Cov.: 59

GnomAD4 exome AF: 0.00000115 AC: 1 AN: 871522 Hom.: 0 Cov.: 98 AF XY: 0.00 AC XY: 0 AN XY: 405014

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

African (AFR) AF: 0.00 AC: 0 AN: 16944

American (AMR) AF: 0.00 AC: 0 AN: 3106

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 6048

East Asian (EAS) AF: 0.00 AC: 0 AN: 5064

South Asian (SAS) AF: 0.00 AC: 0 AN: 21160

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 2012

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 1790

European-Non Finnish (NFE) AF: 0.00000127 AC: 1 AN: 785970

Other (OTH) AF: 0.00 AC: 0 AN: 29428

⚠️ The allele balance in gnomAD4 Exomes is highly skewed from 0.5 (p-value = 0), which strongly suggests a high chance of mosaicism in these individuals.

GnomAD4 genome Cov.: 59

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	1.0
DANN	Benign	0.66
PhyloP100		-0.091
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs7763092; hg19: chr6-349386;