dbSNP rs12985354: CD22:c.2413-41G>A (chr19-35346525-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The NM_001771.4(CD22):c.2413-41G>A variant causes a intron change. The variant allele was found at a frequency of 0.301 in 1,573,200 control chromosomes in the GnomAD database, including 73,023 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 0.32 ( 8387 hom., cov: 32)

Exomes 𝑓: 0.30 ( 64636 hom. )

Consequence

CD22
NM_001771.4 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 3.83

Publications

21 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

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=-0.78).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.395 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.2413-41G>A	intron	N/A	NP_001762.2	P20273-1
CD22	NM_001185099.2		c.2149-41G>A	intron	N/A	NP_001172028.1	P20273-3
CD22	NM_001185100.2		c.*38-41G>A	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.2413-41G>A	intron	N/A	ENSP00000085219.4	P20273-1
CD22	ENST00000536635.6	TSL:1	c.2149-41G>A	intron	N/A	ENSP00000442279.1	P20273-3
CD22	ENST00000544992.6	TSL:1	c.*38-41G>A	intron	N/A	ENSP00000441237.1	P20273-4

Frequencies

GnomAD3 genomes

AF:

0.324

AC:

49185

AN:

152012

Hom.:

8362

Cov.:

show subpopulations

Gnomad AFR

AF:

0.399

Gnomad AMI

AF:

0.303

Gnomad AMR

AF:

0.269

Gnomad ASJ

AF:

0.322

Gnomad EAS

AF:

0.219

Gnomad SAS

AF:

0.215

Gnomad FIN

AF:

0.265

Gnomad MID

AF:

0.307

Gnomad NFE

AF:

0.315

Gnomad OTH

AF:

0.332

GnomAD2 exomes

AF:

0.281

AC:

52619

AN:

187230

AF XY:

0.278

show subpopulations

Gnomad AFR exome

AF:

0.404

Gnomad AMR exome

AF:

0.230

Gnomad ASJ exome

AF:

0.318

Gnomad EAS exome

AF:

0.224

Gnomad FIN exome

AF:

0.264

Gnomad NFE exome

AF:

0.313

Gnomad OTH exome

AF:

0.293

GnomAD4 exome

AF:

0.299

AC:

424775

AN:

1421070

Hom.:

64636

Cov.:

AF XY:

0.296

AC XY:

208324

AN XY:

703366

show subpopulations

African (AFR)

AF:

0.407

AC:

13299

AN:

32658

American (AMR)

AF:

0.236

AC:

9320

AN:

39538

Ashkenazi Jewish (ASJ)

AF:

0.320

AC:

8127

AN:

25418

East Asian (EAS)

AF:

0.185

AC:

7028

AN:

38000

South Asian (SAS)

AF:

0.225

AC:

18419

AN:

81974

European-Finnish (FIN)

AF:

0.270

AC:

13595

AN:

50380

Middle Eastern (MID)

AF:

0.325

AC:

1856

AN:

5716

European-Non Finnish (NFE)

AF:

0.308

AC:

335477

AN:

1088748

Other (OTH)

AF:

0.301

AC:

17654

AN:

58638

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.472

Heterozygous variant carriers

13602

27204

40806

54408

68010

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

11032

22064

33096

44128

55160

<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:

0.324

AC:

49254

AN:

152130

Hom.:

8387

Cov.:

AF XY:

0.318

AC XY:

23680

AN XY:

74364

show subpopulations

African (AFR)

AF:

0.400

AC:

16599

AN:

41472

American (AMR)

AF:

0.269

AC:

4118

AN:

15290

Ashkenazi Jewish (ASJ)

AF:

0.322

AC:

1117

AN:

3470

East Asian (EAS)

AF:

0.219

AC:

1137

AN:

5180

South Asian (SAS)

AF:

0.213

AC:

1029

AN:

4820

European-Finnish (FIN)

AF:

0.265

AC:

2806

AN:

10598

Middle Eastern (MID)

AF:

0.303

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.315

AC:

21382

AN:

67982

Other (OTH)

AF:

0.332

AC:

701

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

1695

3389

5084

6778

8473

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

484

968

1452

1936

2420

<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:

0.310

Hom.:

13278

Bravo

AF:

0.328

Asia WGS

AF:

0.227

AC:

791

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.78

CADD

Benign

(source)

DANN

Benign

0.76

PhyloP100

3.8

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.050

Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

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