dbSNP rs7248108: CD22:c.1249+47A>G (chr19-35338478-A-G) – 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.1249+47A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0442 in 1,578,330 control chromosomes in the GnomAD database, including 3,504 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 0.094 ( 1410 hom., cov: 32)

Exomes 𝑓: 0.039 ( 2094 hom. )

Consequence

CD22
NM_001771.4 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.886

Publications

6 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=-0.91).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.244 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CD22	NM_001771.4 link	c.1249+47A>G		intron_variant	Intron 6 of 13	ENST00000085219.10	NP_001762.2	P20273-1Q0EAF5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CD22	ENST00000085219.10 link	c.1249+47A>G		intron_variant	Intron 6 of 13	1	NM_001771.4	ENSP00000085219.4		P20273-1

Frequencies

GnomAD3 genomes

AF:

0.0943

AC:

14323

AN:

151966

Hom.:

1410

Cov.:

show subpopulations

Gnomad AFR

AF:

0.248

Gnomad AMI

AF:

0.00658

Gnomad AMR

AF:

0.0424

Gnomad ASJ

AF:

0.0219

Gnomad EAS

AF:

0.140

Gnomad SAS

AF:

0.0649

Gnomad FIN

AF:

0.0216

Gnomad MID

AF:

0.0285

Gnomad NFE

AF:

0.0286

Gnomad OTH

AF:

0.0570

GnomAD2 exomes

AF:

0.0555

AC:

12336

AN:

222202

AF XY:

0.0525

show subpopulations

Gnomad AFR exome

AF:

0.255

Gnomad AMR exome

AF:

0.0267

Gnomad ASJ exome

AF:

0.0257

Gnomad EAS exome

AF:

0.147

Gnomad FIN exome

AF:

0.0213

Gnomad NFE exome

AF:

0.0274

Gnomad OTH exome

AF:

0.0335

GnomAD4 exome

AF:

0.0388

AC:

55363

AN:

1426248

Hom.:

2094

Cov.:

AF XY:

0.0386

AC XY:

27194

AN XY:

705350

show subpopulations

African (AFR)

AF:

0.246

AC:

8031

AN:

32654

American (AMR)

AF:

0.0270

AC:

1139

AN:

42224

Ashkenazi Jewish (ASJ)

AF:

0.0223

AC:

532

AN:

23848

East Asian (EAS)

AF:

0.113

AC:

4430

AN:

39376

South Asian (SAS)

AF:

0.0576

AC:

4630

AN:

80366

European-Finnish (FIN)

AF:

0.0236

AC:

1219

AN:

51554

Middle Eastern (MID)

AF:

0.0201

AC:

113

AN:

5634

European-Non Finnish (NFE)

AF:

0.0298

AC:

32503

AN:

1091692

Other (OTH)

AF:

0.0470

AC:

2766

AN:

58900

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.499

Heterozygous variant carriers

2724

5448

8172

10896

13620

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

1482

2964

4446

5928

7410

<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:

0.0944

AC:

14350

AN:

152082

Hom.:

1410

Cov.:

AF XY:

0.0929

AC XY:

6909

AN XY:

74350

show subpopulations

African (AFR)

AF:

0.248

AC:

10280

AN:

41438

American (AMR)

AF:

0.0424

AC:

648

AN:

15286

Ashkenazi Jewish (ASJ)

AF:

0.0219

AC:

AN:

3472

East Asian (EAS)

AF:

0.141

AC:

723

AN:

5132

South Asian (SAS)

AF:

0.0651

AC:

314

AN:

4820

European-Finnish (FIN)

AF:

0.0216

AC:

229

AN:

10616

Middle Eastern (MID)

AF:

0.0238

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0286

AC:

1943

AN:

68002

Other (OTH)

AF:

0.0588

AC:

124

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

589

1178

1766

2355

2944

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

146

292

438

584

730

<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:

0.0480

Hom.:

710

Bravo

AF:

0.101

Asia WGS

AF:

0.112

AC:

391

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.91

CADD

Benign

0.24

(source)

DANN

Benign

0.39

PhyloP100

-0.89

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

Publications

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over