dbSNP rs10419538: CD22:c.412+192C>G (chr19-35333116-C-G) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is . The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001771.4(CD22):c.412+192C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.127 in 565,708 control chromosomes in the GnomAD database, including 5,202 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 0.12 ( 1215 hom., cov: 32)

Exomes 𝑓: 0.13 ( 3987 hom. )

Consequence

CD22
NM_001771.4 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.354

Publications

5 publications found

Variant links:

Genes affected

CD22 (HGNC:1643): (CD22 molecule) Predicted to enable CD4 receptor binding activity; protein phosphatase binding activity; and sialic acid binding activity. Involved in B cell activation; negative regulation of B cell receptor signaling pathway; and regulation of endocytosis. Located in early endosome and recycling endosome. [provided by Alliance of Genome Resources, Apr 2022]

CD22 links:

Genome browser will be placed here

new If you want to explore the variant's impact on the transcript NM_001771.4, check out the Mutation Effect Viewer. This is especially useful for frameshift variants or if you want to visualize the effect of exon loss / intron retention.

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.83).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.183 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001771.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
CD22	NM_001771.4	MANE Select	c.412+192C>G	intron	N/A	NP_001762.2	P20273-1
CD22	NM_001185099.2		c.412+192C>G	intron	N/A	NP_001172028.1	P20273-3
CD22	NM_001185100.2		c.412+192C>G	intron	N/A	NP_001172029.1	P20273-4

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
CD22	ENST00000085219.10	TSL:1 MANE Select	c.412+192C>G	intron	N/A	ENSP00000085219.4	P20273-1
CD22	ENST00000536635.6	TSL:1	c.412+192C>G	intron	N/A	ENSP00000442279.1	P20273-3
CD22	ENST00000544992.6	TSL:1	c.412+192C>G	intron	N/A	ENSP00000441237.1	P20273-4

Frequencies

GnomAD3 genomes

AF:

0.116

AC:

17604

AN:

152142

Hom.:

1217

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0545

Gnomad AMI

AF:

0.249

Gnomad AMR

AF:

0.160

Gnomad ASJ

AF:

0.0919

Gnomad EAS

AF:

0.193

Gnomad SAS

AF:

0.0360

Gnomad FIN

AF:

0.140

Gnomad MID

AF:

0.149

Gnomad NFE

AF:

0.138

Gnomad OTH

AF:

0.126

GnomAD4 exome

AF:

0.131

AC:

54168

AN:

413448

Hom.:

3987

Cov.:

AF XY:

0.127

AC XY:

27204

AN XY:

214138

show subpopulations

African (AFR)

AF:

0.0523

AC:

635

AN:

12144

American (AMR)

AF:

0.146

AC:

2372

AN:

16300

Ashkenazi Jewish (ASJ)

AF:

0.0991

AC:

1286

AN:

12972

East Asian (EAS)

AF:

0.211

AC:

6351

AN:

30092

South Asian (SAS)

AF:

0.0334

AC:

1087

AN:

32514

European-Finnish (FIN)

AF:

0.136

AC:

3806

AN:

28074

Middle Eastern (MID)

AF:

0.106

AC:

200

AN:

1888

European-Non Finnish (NFE)

AF:

0.138

AC:

35192

AN:

254822

Other (OTH)

AF:

0.131

AC:

3239

AN:

24642

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

2237

4475

6712

8950

11187

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

268

536

804

1072

1340

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.116

AC:

17590

AN:

152260

Hom.:

1215

Cov.:

AF XY:

0.117

AC XY:

8698

AN XY:

74452

show subpopulations

African (AFR)

AF:

0.0544

AC:

2263

AN:

41562

American (AMR)

AF:

0.160

AC:

2446

AN:

15288

Ashkenazi Jewish (ASJ)

AF:

0.0919

AC:

319

AN:

3470

East Asian (EAS)

AF:

0.193

AC:

996

AN:

5174

South Asian (SAS)

AF:

0.0363

AC:

175

AN:

4826

European-Finnish (FIN)

AF:

0.140

AC:

1486

AN:

10612

Middle Eastern (MID)

AF:

0.143

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.138

AC:

9375

AN:

68008

Other (OTH)

AF:

0.123

AC:

261

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

796

1592

2388

3184

3980

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

186

372

558

744

930

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.121

Hom.:

161

Bravo

AF:

0.116

Asia WGS

AF:

0.105

AC:

367

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.83

CADD

Benign

2.1

(source)

DANN

Benign

0.73

PhyloP100

-0.35

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over