chr2-233031788-C-T

Variant names:

• chr2-233031788-C-T
• rs2233375
• ENST00000851001.1:c.-4-880C>T

Variant summary

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

The ENST00000851001.1(NEU2):​c.-4-880C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.154 in 152,174 control chromosomes in the GnomAD database, including 2,360 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 0.15 (2360 hom., cov: 33)
• Consequence: NEU2 ENST00000851001.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.197
• Publications: 4 publications found

Genes affected

NEU2 (HGNC:7759): (neuraminidase 2) This gene belongs to a family of glycohydrolytic enzymes which remove sialic acid residues from glycoproteins and glycolipids. Expression studies in COS7 cells confirmed that this gene encodes a functional sialidase. Its cytosolic localization was demonstrated by cell fractionation experiments. [provided by RefSeq, Jul 2008]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.271 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000851001.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NEU2	ENST00000851001.1		c.-4-880C>T		intron	N/A	ENSP00000521075.1

Frequencies

GnomAD3 genomes AF: 0.154 AC: 23464 AN: 152056 Hom.: 2354 Cov.: 33

Gnomad AFR AF: 0.276

Gnomad AMI AF: 0.0881

Gnomad AMR AF: 0.188

Gnomad ASJ AF: 0.0611

Gnomad EAS AF: 0.0104

Gnomad SAS AF: 0.125

Gnomad FIN AF: 0.0879

Gnomad MID AF: 0.0918

Gnomad NFE AF: 0.103

Gnomad OTH AF: 0.129

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

GnomAD4 genome AF: 0.154 AC: 23500 AN: 152174 Hom.: 2360 Cov.: 33 AF XY: 0.152 AC XY: 11282 AN XY: 74412

African (AFR) AF: 0.276 AC: 11432 AN: 41486

American (AMR) AF: 0.189 AC: 2888 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.0611 AC: 212 AN: 3472

East Asian (EAS) AF: 0.0104 AC: 54 AN: 5176

South Asian (SAS) AF: 0.125 AC: 602 AN: 4822

European-Finnish (FIN) AF: 0.0879 AC: 933 AN: 10610

Middle Eastern (MID) AF: 0.0952 AC: 28 AN: 294

European-Non Finnish (NFE) AF: 0.103 AC: 7002 AN: 67996

Other (OTH) AF: 0.127 AC: 269 AN: 2114

Alfa AF: 0.119 Hom.: 2004

Bravo AF: 0.164

Asia WGS AF: 0.0740 AC: 257 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.4
DANN	Benign	0.45
PhyloP100		-0.20

Splicing

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

Other links and lift over

dbSNP: rs2233375; hg19: chr2-233896498;