rs3865444

Variant names:

• chr19-51224706-C-A
• rs3865444
• XM_011527531.3:c.-1C>A

Your query was ambiguous. Multiple possible variants found:

• chr19-51224706-C-A
• chr19-51224706-C-G
• chr19-51224706-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XM_011527531.3(CD33):​c.-1C>A variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.254 in 152,044 control chromosomes in the GnomAD database, including 6,038 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 0.25 (6038 hom., cov: 31)
• Consequence: CD33 XM_011527531.3 5_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.61

Genes affected

CD33 (HGNC:1659): (CD33 molecule) Enables protein phosphatase binding activity and sialic acid binding activity. Involved in several processes, including negative regulation of cytokine production; negative regulation of monocyte activation; and positive regulation of protein tyrosine phosphatase activity. Located in several cellular components, including Golgi apparatus; external side of plasma membrane; and peroxisome. [provided by Alliance of Genome Resources, Apr 2022]

LOC107985327 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.419 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CD33	XM_011527531.3	c.-1C>A		5_prime_UTR_variant	Exon 6 of 13		XP_011525833.1
CD33	XM_017027508.2	c.-1C>A		5_prime_UTR_variant	Exon 6 of 13		XP_016882997.1
CD33	XM_047439728.1	c.-1C>A		5_prime_UTR_variant	Exon 5 of 12		XP_047295684.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.254 AC: 38556 AN: 151926 Hom.: 6026 Cov.: 31

Gnomad AFR AF: 0.0868

Gnomad AMI AF: 0.173

Gnomad AMR AF: 0.427

Gnomad ASJ AF: 0.207

Gnomad EAS AF: 0.187

Gnomad SAS AF: 0.157

Gnomad FIN AF: 0.359

Gnomad MID AF: 0.258

Gnomad NFE AF: 0.316

Gnomad OTH AF: 0.253

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

GnomAD4 genome AF: 0.254 AC: 38576 AN: 152044 Hom.: 6038 Cov.: 31 AF XY: 0.258 AC XY: 19175 AN XY: 74316

Gnomad4 AFR AF: 0.0868

Gnomad4 AMR AF: 0.428

Gnomad4 ASJ AF: 0.207

Gnomad4 EAS AF: 0.188

Gnomad4 SAS AF: 0.156

Gnomad4 FIN AF: 0.359

Gnomad4 NFE AF: 0.316

Gnomad4 OTH AF: 0.250

Alfa AF: 0.302 Hom.: 16394

Bravo AF: 0.255

Asia WGS AF: 0.170 AC: 592 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.25
DANN	Benign	0.48

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3865444; hg19: chr19-51727962;