rs2267574

Variant names:

• chr19-35334240-T-A
• rs2267574
• NM_001771.4:c.412+1316T>A

Your query was ambiguous. Multiple possible variants found:

• chr19-35334240-T-A
• chr19-35334240-T-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.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
• Publications: 6 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=-0.63).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.184 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CD22	NM_001771.4	MANE Select	c.412+1316T>A		intron	N/A	NP_001762.2	P20273-1
	CD22	NM_001185099.2		c.412+1316T>A		intron	N/A	NP_001172028.1	P20273-3
	CD22	NM_001185100.2		c.412+1316T>A		intron	N/A	NP_001172029.1	P20273-4

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CD22	ENST00000085219.10	TSL:1 MANE Select	c.412+1316T>A		intron	N/A	ENSP00000085219.4	P20273-1
	CD22	ENST00000536635.6	TSL:1	c.412+1316T>A		intron	N/A	ENSP00000442279.1	P20273-3
	CD22	ENST00000544992.6	TSL:1	c.412+1316T>A		intron	N/A	ENSP00000441237.1	P20273-4

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

African (AFR) AF: 0.0434 AC: 1803 AN: 41538

American (AMR) AF: 0.170 AC: 2600 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.0861 AC: 299 AN: 3472

East Asian (EAS) AF: 0.194 AC: 1005 AN: 5174

South Asian (SAS) AF: 0.0348 AC: 168 AN: 4824

European-Finnish (FIN) AF: 0.119 AC: 1263 AN: 10580

Middle Eastern (MID) AF: 0.122 AC: 36 AN: 294

European-Non Finnish (NFE) AF: 0.121 AC: 8262 AN: 68000

Other (OTH) AF: 0.109 AC: 230 AN: 2104

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.63
CADD	Benign	12
DANN	Benign	0.92
PhyloP100		0.29
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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs2267574;

hg19: chr19-35825143;