19-35346791-C-T

Variant names:

• chr19-35346791-C-T
• rs73031792
• NM_001771.4:c.*94C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001771.4(CD22):​c.*94C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.175 in 1,155,452 control chromosomes in the GnomAD database, including 19,623 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 0.14 (1997 hom., cov: 32)
  • Exomes 𝑓: 0.18 (17626 hom.)
• Consequence: CD22 NM_001771.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.880
• 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=-0.81).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.202 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CD22	NM_001771.4	c.*94C>T		3_prime_UTR_variant	Exon 14 of 14	ENST00000085219.10	NP_001762.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CD22	ENST00000085219.10	c.*94C>T		3_prime_UTR_variant	Exon 14 of 14	1	NM_001771.4	ENSP00000085219.4

Frequencies

GnomAD3 genomes AF: 0.142 AC: 21474 AN: 151520 Hom.: 1997 Cov.: 32

Gnomad AFR AF: 0.0405

Gnomad AMI AF: 0.157

Gnomad AMR AF: 0.162

Gnomad ASJ AF: 0.209

Gnomad EAS AF: 0.00270

Gnomad SAS AF: 0.212

Gnomad FIN AF: 0.157

Gnomad MID AF: 0.133

Gnomad NFE AF: 0.198

Gnomad OTH AF: 0.148

GnomAD4 exome AF: 0.180 AC: 180489 AN: 1003816 Hom.: 17626 Cov.: 14 AF XY: 0.182 AC XY: 90969 AN XY: 501006

African (AFR) AF: 0.0340 AC: 808 AN: 23752

American (AMR) AF: 0.191 AC: 4860 AN: 25380

Ashkenazi Jewish (ASJ) AF: 0.210 AC: 3769 AN: 17928

East Asian (EAS) AF: 0.00104 AC: 36 AN: 34622

South Asian (SAS) AF: 0.225 AC: 13744 AN: 61014

European-Finnish (FIN) AF: 0.165 AC: 6942 AN: 42050

Middle Eastern (MID) AF: 0.172 AC: 541 AN: 3146

European-Non Finnish (NFE) AF: 0.189 AC: 142253 AN: 751664

Other (OTH) AF: 0.170 AC: 7536 AN: 44260

GnomAD4 genome AF: 0.142 AC: 21485 AN: 151636 Hom.: 1997 Cov.: 32 AF XY: 0.142 AC XY: 10505 AN XY: 74124

African (AFR) AF: 0.0404 AC: 1658 AN: 41028

American (AMR) AF: 0.163 AC: 2489 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.209 AC: 726 AN: 3470

East Asian (EAS) AF: 0.00290 AC: 15 AN: 5174

South Asian (SAS) AF: 0.213 AC: 1025 AN: 4818

European-Finnish (FIN) AF: 0.157 AC: 1659 AN: 10588

Middle Eastern (MID) AF: 0.129 AC: 38 AN: 294

European-Non Finnish (NFE) AF: 0.198 AC: 13425 AN: 67956

Other (OTH) AF: 0.145 AC: 307 AN: 2110

Alfa AF: 0.128 Hom.: 650

Bravo AF: 0.134

Asia WGS AF: 0.0950 AC: 334 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	0.35
DANN	Benign	0.64
PhyloP100		-0.88
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: rs73031792; hg19: chr19-35837694; COSMIC: COSV50060971; COSMIC: COSV50060971;