19-35345923-C-G

Variant names:

• chr19-35345923-C-G
• rs10413500
• NM_001771.4:c.2327+203C>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.2327+203C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.164 in 152,222 control chromosomes in the GnomAD database, including 2,259 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 0.16 (2259 hom., cov: 32)
• Consequence: CD22 NM_001771.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.528
• Publications: 5 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=-0.81).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.276 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.2327+203C>G		intron	N/A	NP_001762.2	P20273-1
	CD22	NM_001185099.2		c.2063+203C>G		intron	N/A	NP_001172028.1	P20273-3
	CD22	NM_001185100.2		c.2209-228C>G		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.2327+203C>G		intron	N/A	ENSP00000085219.4	P20273-1
	CD22	ENST00000536635.6	TSL:1	c.2063+203C>G		intron	N/A	ENSP00000442279.1	P20273-3
	CD22	ENST00000544992.6	TSL:1	c.2209-228C>G		intron	N/A	ENSP00000441237.1	P20273-4

Frequencies

GnomAD3 genomes AF: 0.163 AC: 24856 AN: 152104 Hom.: 2250 Cov.: 32

Gnomad AFR AF: 0.212

Gnomad AMI AF: 0.148

Gnomad AMR AF: 0.179

Gnomad ASJ AF: 0.213

Gnomad EAS AF: 0.0564

Gnomad SAS AF: 0.287

Gnomad FIN AF: 0.120

Gnomad MID AF: 0.218

Gnomad NFE AF: 0.134

Gnomad OTH AF: 0.164

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

GnomAD4 genome AF: 0.164 AC: 24895 AN: 152222 Hom.: 2259 Cov.: 32 AF XY: 0.166 AC XY: 12324 AN XY: 74422

African (AFR) AF: 0.212 AC: 8813 AN: 41522

American (AMR) AF: 0.179 AC: 2740 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.213 AC: 740 AN: 3472

East Asian (EAS) AF: 0.0567 AC: 294 AN: 5182

South Asian (SAS) AF: 0.289 AC: 1393 AN: 4826

European-Finnish (FIN) AF: 0.120 AC: 1275 AN: 10618

Middle Eastern (MID) AF: 0.218 AC: 64 AN: 294

European-Non Finnish (NFE) AF: 0.134 AC: 9097 AN: 68004

Other (OTH) AF: 0.163 AC: 344 AN: 2108

Alfa AF: 0.160 Hom.: 266

Bravo AF: 0.167

Asia WGS AF: 0.205 AC: 715 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	11
DANN	Benign	0.75
PhyloP100		0.53
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: rs10413500; hg19: chr19-35836826;