19-35334240-T-A

Position:

• chr19-35334240-T-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001771.4(CD22):​c.412+1316T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.104 in 152,182 control chromosomes in the GnomAD database, including 1,028 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 0.10 (1028 hom., cov: 32)
• Consequence: CD22 NM_001771.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.293

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=-0.63).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.184 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CD22	NM_001771.4	c.412+1316T>A		intron_variant		ENST00000085219.10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CD22	ENST00000085219.10	c.412+1316T>A		intron_variant		1	NM_001771.4	P2

Frequencies

GnomAD3 genomes AF: 0.104 AC: 15794 AN: 152064 Hom.: 1030 Cov.: 32

Gnomad AFR AF: 0.0435

Gnomad AMI AF: 0.126

Gnomad AMR AF: 0.170

Gnomad ASJ AF: 0.0861

Gnomad EAS AF: 0.195

Gnomad SAS AF: 0.0346

Gnomad FIN AF: 0.119

Gnomad MID AF: 0.130

Gnomad NFE AF: 0.122

Gnomad OTH AF: 0.112

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

GnomAD4 genome AF: 0.104 AC: 15781 AN: 152182 Hom.: 1028 Cov.: 32 AF XY: 0.105 AC XY: 7806 AN XY: 74410

Gnomad4 AFR AF: 0.0434

Gnomad4 AMR AF: 0.170

Gnomad4 ASJ AF: 0.0861

Gnomad4 EAS AF: 0.194

Gnomad4 SAS AF: 0.0348

Gnomad4 FIN AF: 0.119

Gnomad4 NFE AF: 0.121

Gnomad4 OTH AF: 0.109

Alfa AF: 0.109 Hom.: 138

Bravo AF: 0.105

Asia WGS AF: 0.106 AC: 369 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.63
CADD	Benign	12
DANN	Benign	0.92

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: rs2267574; hg19: chr19-35825143;