rs10413526

Variant names:

• chr19-35345952-C-G
• rs10413526
• NM_001771.4:c.2328-199C>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001771.4(CD22):​c.2328-199C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.336 in 152,014 control chromosomes in the GnomAD database, including 8,877 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 0.34 (8877 hom., cov: 32)
• Consequence: CD22 NM_001771.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.24
• Publications: 4 publications found

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]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.392 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CD22	NM_001771.4	MANE Select	c.2328-199C>G		intron	N/A	NP_001762.2
	CD22	NM_001185099.2		c.2064-199C>G		intron	N/A	NP_001172028.1
	CD22	NM_001185100.2		c.2209-199C>G		intron	N/A	NP_001172029.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CD22	ENST00000085219.10	TSL:1 MANE Select	c.2328-199C>G		intron	N/A	ENSP00000085219.4
	CD22	ENST00000536635.6	TSL:1	c.2064-199C>G		intron	N/A	ENSP00000442279.1
	CD22	ENST00000544992.6	TSL:1	c.2209-199C>G		intron	N/A	ENSP00000441237.1

Frequencies

GnomAD3 genomes AF: 0.336 AC: 51039 AN: 151896 Hom.: 8864 Cov.: 32

Gnomad AFR AF: 0.397

Gnomad AMI AF: 0.540

Gnomad AMR AF: 0.258

Gnomad ASJ AF: 0.351

Gnomad EAS AF: 0.402

Gnomad SAS AF: 0.251

Gnomad FIN AF: 0.343

Gnomad MID AF: 0.339

Gnomad NFE AF: 0.313

Gnomad OTH AF: 0.330

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.336 AC: 51094 AN: 152014 Hom.: 8877 Cov.: 32 AF XY: 0.334 AC XY: 24782 AN XY: 74302

African (AFR) AF: 0.397 AC: 16472 AN: 41446

American (AMR) AF: 0.258 AC: 3941 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.351 AC: 1219 AN: 3472

East Asian (EAS) AF: 0.402 AC: 2077 AN: 5162

South Asian (SAS) AF: 0.250 AC: 1205 AN: 4828

European-Finnish (FIN) AF: 0.343 AC: 3632 AN: 10590

Middle Eastern (MID) AF: 0.337 AC: 99 AN: 294

European-Non Finnish (NFE) AF: 0.313 AC: 21249 AN: 67942

Other (OTH) AF: 0.337 AC: 711 AN: 2108

Alfa AF: 0.325 Hom.: 1035

Bravo AF: 0.335

Asia WGS AF: 0.339 AC: 1178 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.54
DANN	Benign	0.59
PhyloP100		-1.2
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs10413526; hg19: chr19-35836855;