rs624786

Variant names:

• chr11-74982984-T-G
• rs624786
• XM_047426298.1:c.-1451T>G

Variant summary

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

The XM_047426298.1(NEU3):​c.-1451T>G variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.405 in 151,752 control chromosomes in the GnomAD database, including 13,301 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 0.41 (13301 hom., cov: 31)
• Consequence: NEU3 XM_047426298.1 5_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.318
• Publications: 13 publications found

Genes affected

NEU3 (HGNC:7760): (neuraminidase 3) This gene product belongs to a family of glycohydrolytic enzymes which remove sialic acid residues from glycoproteins and glycolipids. It is localized in the plasma membrane, and its activity is specific for gangliosides. It may play a role in modulating the ganglioside content of the lipid bilayer. [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=-0.74).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.49 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.406 AC: 61496 AN: 151634 Hom.: 13306 Cov.: 31

Gnomad AFR AF: 0.284

Gnomad AMI AF: 0.608

Gnomad AMR AF: 0.326

Gnomad ASJ AF: 0.451

Gnomad EAS AF: 0.198

Gnomad SAS AF: 0.478

Gnomad FIN AF: 0.449

Gnomad MID AF: 0.525

Gnomad NFE AF: 0.495

Gnomad OTH AF: 0.435

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

GnomAD4 genome AF: 0.405 AC: 61502 AN: 151752 Hom.: 13301 Cov.: 31 AF XY: 0.402 AC XY: 29779 AN XY: 74132

African (AFR) AF: 0.283 AC: 11714 AN: 41330

American (AMR) AF: 0.325 AC: 4967 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.451 AC: 1564 AN: 3468

East Asian (EAS) AF: 0.198 AC: 1017 AN: 5138

South Asian (SAS) AF: 0.478 AC: 2301 AN: 4810

European-Finnish (FIN) AF: 0.449 AC: 4711 AN: 10502

Middle Eastern (MID) AF: 0.507 AC: 149 AN: 294

European-Non Finnish (NFE) AF: 0.495 AC: 33614 AN: 67934

Other (OTH) AF: 0.433 AC: 912 AN: 2106

Alfa AF: 0.467 Hom.: 8987

Bravo AF: 0.387

Asia WGS AF: 0.340 AC: 1183 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.74
CADD	Benign	3.0
DANN	Benign	0.87
PhyloP100		-0.32

Splicing

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

Other links and lift over

dbSNP: rs624786; hg19: chr11-74694029;