dbSNP rs3088063: CD22:c.*476C>T (chr19-35347173-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.*476C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0849 in 155,996 control chromosomes in the GnomAD database, including 668 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 0.085 ( 642 hom., cov: 32)

Exomes 𝑓: 0.072 ( 26 hom. )

Consequence

CD22
NM_001771.4 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0380

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=-0.87).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.209 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
CD22	NM_001771.4	MANE Select	c.*476C>T	3_prime_UTR	Exon 14 of 14	NP_001762.2
CD22	NM_001185099.2		c.*476C>T	3_prime_UTR	Exon 13 of 13	NP_001172028.1
CD22	NM_001185100.2		c.*645C>T	3_prime_UTR	Exon 13 of 13	NP_001172029.1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
CD22	ENST00000085219.10	TSL:1 MANE Select	c.*476C>T	3_prime_UTR	Exon 14 of 14	ENSP00000085219.4
CD22	ENST00000536635.6	TSL:1	c.*476C>T	3_prime_UTR	Exon 13 of 13	ENSP00000442279.1
CD22	ENST00000601769.5	TSL:2	n.*2325C>T	non_coding_transcript_exon	Exon 14 of 14	ENSP00000470193.1

Frequencies

GnomAD3 genomes

AF:

0.0850

AC:

12922

AN:

152032

Hom.:

630

Cov.:

show subpopulations

Gnomad AFR

AF:

0.118

Gnomad AMI

AF:

0.185

Gnomad AMR

AF:

0.0564

Gnomad ASJ

AF:

0.0671

Gnomad EAS

AF:

0.110

Gnomad SAS

AF:

0.219

Gnomad FIN

AF:

0.0542

Gnomad MID

AF:

0.104

Gnomad NFE

AF:

0.0645

Gnomad OTH

AF:

0.0742

GnomAD4 exome

AF:

0.0718

AC:

276

AN:

3844

Hom.:

Cov.:

AF XY:

0.0864

AC XY:

181

AN XY:

2094

show subpopulations

African (AFR)

AF:

0.0714

AC:

AN:

American (AMR)

AF:

0.0380

AC:

AN:

790

Ashkenazi Jewish (ASJ)

AF:

0.0385

AC:

AN:

East Asian (EAS)

AF:

0.125

AC:

AN:

South Asian (SAS)

AF:

0.189

AC:

131

AN:

694

European-Finnish (FIN)

AF:

0.0313

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.0484

AC:

103

AN:

2126

Other (OTH)

AF:

0.0435

AC:

AN:

138

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.517

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

<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:

0.0852

AC:

12966

AN:

152152

Hom.:

642

Cov.:

AF XY:

0.0873

AC XY:

6495

AN XY:

74378

show subpopulations

African (AFR)

AF:

0.118

AC:

4909

AN:

41486

American (AMR)

AF:

0.0563

AC:

861

AN:

15280

Ashkenazi Jewish (ASJ)

AF:

0.0671

AC:

233

AN:

3472

East Asian (EAS)

AF:

0.110

AC:

569

AN:

5164

South Asian (SAS)

AF:

0.220

AC:

1061

AN:

4826

European-Finnish (FIN)

AF:

0.0542

AC:

574

AN:

10588

Middle Eastern (MID)

AF:

0.109

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0645

AC:

4385

AN:

68020

Other (OTH)

AF:

0.0820

AC:

173

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

615

1231

1846

2462

3077

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

154

308

462

616

770

<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:

0.0697

Hom.:

1121

Bravo

AF:

0.0835

Asia WGS

AF:

0.206

AC:

716

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.87

CADD

Benign

4.8

(source)

DANN

Benign

0.61

PhyloP100

-0.038

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

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over