19-35346820-A-ACG

Variant names:

• chr19-35346820-A-ACG
• rs34472317
• NM_001771.4:c.*124_*125insGC

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BA1

The NM_001771.4(CD22):​c.*124_*125insGC variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0756 in 425,680 control chromosomes in the GnomAD database, including 1,486 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.084 (1081 hom., cov: 31)
  • Exomes 𝑓: 0.071 (405 hom.)
• Consequence: CD22 NM_001771.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.174
• Publications: 2 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 -8 ACMG points.

• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.221 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.*124_*125insGC		3_prime_UTR	Exon 14 of 14	NP_001762.2	P20273-1
	CD22	NM_001185099.2		c.*124_*125insGC		3_prime_UTR	Exon 13 of 13	NP_001172028.1	P20273-3
	CD22	NM_001185100.2		c.*293_*294insGC		3_prime_UTR	Exon 13 of 13	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.*124_*125insGC		3_prime_UTR	Exon 14 of 14	ENSP00000085219.4	P20273-1
	CD22	ENST00000536635.6	TSL:1	c.*124_*125insGC		3_prime_UTR	Exon 13 of 13	ENSP00000442279.1	P20273-3
	CD22	ENST00000544992.6	TSL:1	c.*293_*294insGC		3_prime_UTR	Exon 13 of 13	ENSP00000441237.1	P20273-4

Frequencies

GnomAD3 genomes AF: 0.0833 AC: 12484 AN: 149926 Hom.: 1065 Cov.: 31

Gnomad AFR AF: 0.224

Gnomad AMI AF: 0.139

Gnomad AMR AF: 0.0457

Gnomad ASJ AF: 0.0387

Gnomad EAS AF: 0.0666

Gnomad SAS AF: 0.0847

Gnomad FIN AF: 0.0212

Gnomad MID AF: 0.0545

Gnomad NFE AF: 0.0184

Gnomad OTH AF: 0.0813

GnomAD4 exome AF: 0.0713 AC: 19652 AN: 275654 Hom.: 405 Cov.: 9 AF XY: 0.0745 AC XY: 10486 AN XY: 140776

African (AFR) AF: 0.332 AC: 3466 AN: 10444

American (AMR) AF: 0.0789 AC: 593 AN: 7516

Ashkenazi Jewish (ASJ) AF: 0.109 AC: 601 AN: 5538

East Asian (EAS) AF: 0.129 AC: 1579 AN: 12236

South Asian (SAS) AF: 0.143 AC: 3615 AN: 25250

European-Finnish (FIN) AF: 0.0543 AC: 682 AN: 12560

Middle Eastern (MID) AF: 0.112 AC: 111 AN: 994

European-Non Finnish (NFE) AF: 0.0402 AC: 7550 AN: 187656

Other (OTH) AF: 0.108 AC: 1455 AN: 13460

GnomAD4 genome AF: 0.0837 AC: 12550 AN: 150026 Hom.: 1081 Cov.: 31 AF XY: 0.0827 AC XY: 6060 AN XY: 73250

African (AFR) AF: 0.225 AC: 9205 AN: 40988

American (AMR) AF: 0.0455 AC: 688 AN: 15120

Ashkenazi Jewish (ASJ) AF: 0.0387 AC: 133 AN: 3436

East Asian (EAS) AF: 0.0670 AC: 343 AN: 5118

South Asian (SAS) AF: 0.0846 AC: 403 AN: 4762

European-Finnish (FIN) AF: 0.0212 AC: 216 AN: 10206

Middle Eastern (MID) AF: 0.0586 AC: 17 AN: 290

European-Non Finnish (NFE) AF: 0.0184 AC: 1236 AN: 67122

Other (OTH) AF: 0.0878 AC: 182 AN: 2072

Alfa AF: 0.0144 Hom.: 8

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		-0.17
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs34472317; hg19: chr19-35837723;