rs10413526

chr19-35345952-C-G

Variant summary

Our verdict is Benign. Variant got -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

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

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CD22	NM_001771.4	c.2328-199C>G		intron_variant		ENST00000085219.10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CD22	ENST00000085219.10	c.2328-199C>G		intron_variant		1	NM_001771.4	P2

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

Gnomad4 AFR AF: 0.397

Gnomad4 AMR AF: 0.258

Gnomad4 ASJ AF: 0.351

Gnomad4 EAS AF: 0.402

Gnomad4 SAS AF: 0.250

Gnomad4 FIN AF: 0.343

Gnomad4 NFE AF: 0.313

Gnomad4 OTH AF: 0.337

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 v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
Cadd	Benign	0.54
Dann	Benign	0.59

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

LitVar

Other links and lift over

dbSNP: rs10413526; hg19: chr19-35836855;