rs34472317

Positions:

• chr19-35346820-A-ACG
• chr19-35346820-A-ACGCACACACACACACACACGCACGCACACACACACACACACGCACG
• chr19-35346820-A-ACGCACG

Variant summary

Our verdict is Benign. Variant got -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

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 -8 ACMG points.

• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.221 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CD22	NM_001771.4	c.*124_*125insGC		3_prime_UTR_variant	14/14	ENST00000085219.10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CD22	ENST00000085219.10	c.*124_*125insGC		3_prime_UTR_variant	14/14	1	NM_001771.4	P2

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

Gnomad4 AFR exome AF: 0.332

Gnomad4 AMR exome AF: 0.0789

Gnomad4 ASJ exome AF: 0.109

Gnomad4 EAS exome AF: 0.129

Gnomad4 SAS exome AF: 0.143

Gnomad4 FIN exome AF: 0.0543

Gnomad4 NFE exome AF: 0.0402

Gnomad4 OTH exome AF: 0.108

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

Gnomad4 AFR AF: 0.225

Gnomad4 AMR AF: 0.0455

Gnomad4 ASJ AF: 0.0387

Gnomad4 EAS AF: 0.0670

Gnomad4 SAS AF: 0.0846

Gnomad4 FIN AF: 0.0212

Gnomad4 NFE AF: 0.0184

Gnomad4 OTH AF: 0.0878

Alfa AF: 0.0144 Hom.: 8

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs34472317; hg19: chr19-35837723;