Variant rs34472317 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1

The NM_001771.4(CD22):c.*124_*125insGC variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0756 in 425,680 control chromosomes in the GnomAD database, including 1,486 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.084 ( 1081 hom., cov: 31)

Exomes 𝑓: 0.071 ( 405 hom. )

Consequence

CD22
NM_001771.4 3_prime_UTR

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.174

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:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -8 ACMG points.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.221 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CD22	NM_001771.4 linkuse as main transcript	c.124_125insGC		3_prime_UTR_variant	14/14	ENST00000085219.10	NP_001762.2	P20273-1Q0EAF5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CD22	ENST00000085219.10 linkuse as main transcript	c.124_125insGC		3_prime_UTR_variant	14/14	1	NM_001771.4	ENSP00000085219.4		P20273-1

Frequencies

GnomAD3 genomes

AF:

0.0833

AC:

12484

AN:

149926

Hom.:

1065

Cov.:

show subpopulations

Gnomad AFR

AF:

0.224

Gnomad AMI

AF:

0.139

Gnomad AMR

AF:

0.0457

Gnomad ASJ

AF:

0.0387

Gnomad EAS

AF:

0.0666

Gnomad SAS

AF:

0.0847

Gnomad FIN

AF:

0.0212

Gnomad MID

AF:

0.0545

Gnomad NFE

AF:

0.0184

Gnomad OTH

AF:

0.0813

GnomAD4 exome

AF:

0.0713

AC:

19652

AN:

275654

Hom.:

405

Cov.:

AF XY:

0.0745

AC XY:

10486

AN XY:

140776

show subpopulations

Gnomad4 AFR exome

AF:

0.332

Gnomad4 AMR exome

AF:

0.0789

Gnomad4 ASJ exome

AF:

0.109

Gnomad4 EAS exome

AF:

0.129

Gnomad4 SAS exome

AF:

0.143

Gnomad4 FIN exome

AF:

0.0543

Gnomad4 NFE exome

AF:

0.0402

Gnomad4 OTH exome

AF:

0.108

GnomAD4 genome

AF:

0.0837

AC:

12550

AN:

150026

Hom.:

1081

Cov.:

AF XY:

0.0827

AC XY:

6060

AN XY:

73250

show subpopulations

Gnomad4 AFR

AF:

0.225

Gnomad4 AMR

AF:

0.0455

Gnomad4 ASJ

AF:

0.0387

Gnomad4 EAS

AF:

0.0670

Gnomad4 SAS

AF:

0.0846

Gnomad4 FIN

AF:

0.0212

Gnomad4 NFE

AF:

0.0184

Gnomad4 OTH

AF:

0.0878

Alfa

AF:

0.0144

Hom.:

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

Splicing

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over