19-35333096-C-T

Position:

• chr19-35333096-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The NM_001771.4(CD22):​c.412+172C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0216 in 618,712 control chromosomes in the GnomAD database, including 222 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 0.019 (43 hom., cov: 32)
  • Exomes 𝑓: 0.022 (179 hom.)
• Consequence: CD22 NM_001771.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.489

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 -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BS1: Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.019 (2897/152290) while in subpopulation NFE AF= 0.0267 (1818/68018). AF 95% confidence interval is 0.0257. There are 43 homozygotes in gnomad4. There are 1507 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd4 at 43 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CD22	NM_001771.4	c.412+172C>T		intron_variant		ENST00000085219.10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CD22	ENST00000085219.10	c.412+172C>T		intron_variant		1	NM_001771.4	P2

Frequencies

GnomAD3 genomes AF: 0.0190 AC: 2898 AN: 152172 Hom.: 43 Cov.: 32

Gnomad AFR AF: 0.00352

Gnomad AMI AF: 0.00549

Gnomad AMR AF: 0.00740

Gnomad ASJ AF: 0.0213

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.0170

Gnomad FIN AF: 0.0586

Gnomad MID AF: 0.0316

Gnomad NFE AF: 0.0267

Gnomad OTH AF: 0.0134

GnomAD4 exome AF: 0.0224 AC: 10438 AN: 466422 Hom.: 179 Cov.: 6 AF XY: 0.0224 AC XY: 5388 AN XY: 241006

Gnomad4 AFR exome AF: 0.00374

Gnomad4 AMR exome AF: 0.00702

Gnomad4 ASJ exome AF: 0.0205

Gnomad4 EAS exome AF: 0.0000980

Gnomad4 SAS exome AF: 0.0175

Gnomad4 FIN exome AF: 0.0478

Gnomad4 NFE exome AF: 0.0247

Gnomad4 OTH exome AF: 0.0206

GnomAD4 genome AF: 0.0190 AC: 2897 AN: 152290 Hom.: 43 Cov.: 32 AF XY: 0.0202 AC XY: 1507 AN XY: 74462

Gnomad4 AFR AF: 0.00351

Gnomad4 AMR AF: 0.00739

Gnomad4 ASJ AF: 0.0213

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.0170

Gnomad4 FIN AF: 0.0586

Gnomad4 NFE AF: 0.0267

Gnomad4 OTH AF: 0.0128

Alfa AF: 0.0214 Hom.: 6

Bravo AF: 0.0146

Asia WGS AF: 0.00635 AC: 22 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.8
DANN	Benign	0.90

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

Publications

LitVar

Other links and lift over

dbSNP: rs881456; hg19: chr19-35823999;