rs4805120

Variant names:

• chr19-35345956-A-G
• rs4805120
• NM_001771.4:c.2328-195A>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.2328-195A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.745 in 152,016 control chromosomes in the GnomAD database, including 42,861 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 0.74 (42861 hom., cov: 32)
• Consequence: CD22 NM_001771.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.156
• 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=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.882 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CD22	NM_001771.4	c.2328-195A>G		intron_variant	Intron 12 of 13	ENST00000085219.10	NP_001762.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CD22	ENST00000085219.10	c.2328-195A>G		intron_variant	Intron 12 of 13	1	NM_001771.4	ENSP00000085219.4

Frequencies

GnomAD3 genomes AF: 0.745 AC: 113105 AN: 151898 Hom.: 42808 Cov.: 32

Gnomad AFR AF: 0.890

Gnomad AMI AF: 0.779

Gnomad AMR AF: 0.664

Gnomad ASJ AF: 0.773

Gnomad EAS AF: 0.726

Gnomad SAS AF: 0.737

Gnomad FIN AF: 0.682

Gnomad MID AF: 0.722

Gnomad NFE AF: 0.685

Gnomad OTH AF: 0.721

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

GnomAD4 genome AF: 0.745 AC: 113216 AN: 152016 Hom.: 42861 Cov.: 32 AF XY: 0.743 AC XY: 55205 AN XY: 74288

African (AFR) AF: 0.890 AC: 36903 AN: 41478

American (AMR) AF: 0.664 AC: 10132 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.773 AC: 2684 AN: 3470

East Asian (EAS) AF: 0.727 AC: 3745 AN: 5154

South Asian (SAS) AF: 0.738 AC: 3552 AN: 4816

European-Finnish (FIN) AF: 0.682 AC: 7205 AN: 10568

Middle Eastern (MID) AF: 0.711 AC: 209 AN: 294

European-Non Finnish (NFE) AF: 0.685 AC: 46547 AN: 67950

Other (OTH) AF: 0.725 AC: 1532 AN: 2114

Alfa AF: 0.713 Hom.: 7935

Bravo AF: 0.750

Asia WGS AF: 0.766 AC: 2667 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.9
DANN	Benign	0.62
PhyloP100		-0.16
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: rs4805120; hg19: chr19-35836859;