dbSNP rs45453699: CD22:c.2133-14C>T (chr19-35345037-C-T) – 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.2133-14C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.272 in 1,611,370 control chromosomes in the GnomAD database, including 61,394 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 0.31 ( 7907 hom., cov: 31)

Exomes 𝑓: 0.27 ( 53487 hom. )

Consequence

CD22
NM_001771.4 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.74

Publications

9 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=-0.81).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.405 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CD22	NM_001771.4 link	c.2133-14C>T		intron_variant	Intron 10 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.2133-14C>T		intron_variant	Intron 10 of 13	1	NM_001771.4	ENSP00000085219.4		P20273-1

Frequencies

GnomAD3 genomes

AF:

0.315

AC:

47791

AN:

151824

Hom.:

7898

Cov.:

show subpopulations

Gnomad AFR

AF:

0.410

Gnomad AMI

AF:

0.199

Gnomad AMR

AF:

0.365

Gnomad ASJ

AF:

0.288

Gnomad EAS

AF:

0.278

Gnomad SAS

AF:

0.255

Gnomad FIN

AF:

0.209

Gnomad MID

AF:

0.360

Gnomad NFE

AF:

0.271

Gnomad OTH

AF:

0.338

GnomAD2 exomes

AF:

0.282

AC:

70944

AN:

251452

AF XY:

0.275

show subpopulations

Gnomad AFR exome

AF:

0.417

Gnomad AMR exome

AF:

0.355

Gnomad ASJ exome

AF:

0.284

Gnomad EAS exome

AF:

0.266

Gnomad FIN exome

AF:

0.216

Gnomad NFE exome

AF:

0.268

Gnomad OTH exome

AF:

0.299

GnomAD4 exome

AF:

0.268

AC:

390952

AN:

1459428

Hom.:

53487

Cov.:

AF XY:

0.267

AC XY:

193741

AN XY:

726210

show subpopulations

African (AFR)

AF:

0.415

AC:

13869

AN:

33422

American (AMR)

AF:

0.361

AC:

16122

AN:

44718

Ashkenazi Jewish (ASJ)

AF:

0.287

AC:

7483

AN:

26112

East Asian (EAS)

AF:

0.296

AC:

11766

AN:

39690

South Asian (SAS)

AF:

0.230

AC:

19812

AN:

86190

European-Finnish (FIN)

AF:

0.212

AC:

11318

AN:

53408

Middle Eastern (MID)

AF:

0.346

AC:

1993

AN:

5762

European-Non Finnish (NFE)

AF:

0.263

AC:

291851

AN:

1109816

Other (OTH)

AF:

0.278

AC:

16738

AN:

60310

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.471

Heterozygous variant carriers

13573

27147

40720

54294

67867

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

9868

19736

29604

39472

49340

<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:

0.315

AC:

47832

AN:

151942

Hom.:

7907

Cov.:

AF XY:

0.310

AC XY:

23043

AN XY:

74242

show subpopulations

African (AFR)

AF:

0.410

AC:

16994

AN:

41424

American (AMR)

AF:

0.365

AC:

5567

AN:

15264

Ashkenazi Jewish (ASJ)

AF:

0.288

AC:

999

AN:

3468

East Asian (EAS)

AF:

0.278

AC:

1430

AN:

5152

South Asian (SAS)

AF:

0.255

AC:

1227

AN:

4814

European-Finnish (FIN)

AF:

0.209

AC:

2205

AN:

10560

Middle Eastern (MID)

AF:

0.373

AC:

109

AN:

292

European-Non Finnish (NFE)

AF:

0.271

AC:

18416

AN:

67950

Other (OTH)

AF:

0.334

AC:

704

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

1664

3328

4993

6657

8321

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

476

952

1428

1904

2380

<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:

0.298

Hom.:

3389

Bravo

AF:

0.332

Asia WGS

AF:

0.251

AC:

870

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.81

CADD

Benign

0.41

(source)

DANN

Benign

0.48

PhyloP100

-1.7

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

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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