rs13386477

Variant names:

• chr2-233029786-G-A
• rs13386477
• ENST00000851001.1:c.-4-2882G>A

Your query was ambiguous. Multiple possible variants found:

• chr2-233029786-G-A
• chr2-233029786-G-C

Variant summary

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

The ENST00000851001.1(NEU2):​c.-4-2882G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.782 in 152,166 control chromosomes in the GnomAD database, including 46,681 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 0.78 (46681 hom., cov: 33)
• Consequence: NEU2 ENST00000851001.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.602
• Publications: 6 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=-0.96).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.801 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.-4-2882G>A		intron	N/A	ENSP00000521075.1

Frequencies

GnomAD3 genomes AF: 0.782 AC: 118883 AN: 152048 Hom.: 46638 Cov.: 33

Gnomad AFR AF: 0.775

Gnomad AMI AF: 0.632

Gnomad AMR AF: 0.757

Gnomad ASJ AF: 0.739

Gnomad EAS AF: 0.643

Gnomad SAS AF: 0.751

Gnomad FIN AF: 0.791

Gnomad MID AF: 0.807

Gnomad NFE AF: 0.807

Gnomad OTH AF: 0.777

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

GnomAD4 genome AF: 0.782 AC: 118980 AN: 152166 Hom.: 46681 Cov.: 33 AF XY: 0.778 AC XY: 57831 AN XY: 74372

African (AFR) AF: 0.775 AC: 32174 AN: 41492

American (AMR) AF: 0.757 AC: 11567 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.739 AC: 2567 AN: 3472

East Asian (EAS) AF: 0.643 AC: 3322 AN: 5168

South Asian (SAS) AF: 0.753 AC: 3633 AN: 4826

European-Finnish (FIN) AF: 0.791 AC: 8378 AN: 10598

Middle Eastern (MID) AF: 0.810 AC: 238 AN: 294

European-Non Finnish (NFE) AF: 0.807 AC: 54891 AN: 68008

Other (OTH) AF: 0.773 AC: 1635 AN: 2114

Alfa AF: 0.798 Hom.: 218369

Bravo AF: 0.777

Asia WGS AF: 0.681 AC: 2370 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.98
DANN	Benign	0.24
PhyloP100		-0.60

Splicing

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

Other links and lift over

dbSNP: rs13386477; hg19: chr2-233894496;