NM_001167600.3:c.*568T>C

Variant names:

• chr2-241817616-T-C
• rs16747
• NM_001167600.3:c.*568T>C

Variant summary

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

The NM_001167600.3(NEU4):​c.*568T>C variant causes a downstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.587 in 152,030 control chromosomes in the GnomAD database, including 26,459 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 0.59 (26459 hom., cov: 33)
• Consequence: NEU4 NM_001167600.3 downstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.00

Genes affected

NEU4 (HGNC:21328): (neuraminidase 4) The protein encoded by this gene belongs to a family of glycohydrolytic enzymes, which remove terminal sialic acid residues from various sialo derivatives, such as glycoproteins, glycolipids, oligosaccharides, and gangliosides. Alternatively spliced transcript variants encoding different isoforms have been noted for this gene. [provided by RefSeq, Nov 2009]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (Cadd=1.11).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.626 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
NEU4	NM_001167600.3	c.*568T>C		downstream_gene_variant		ENST00000407683.6	NP_001161072.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
NEU4	ENST00000407683.6	c.*568T>C		downstream_gene_variant		2	NM_001167600.3	ENSP00000385402.1

Frequencies

GnomAD3 genomes AF: 0.587 AC: 89186 AN: 151912 Hom.: 26443 Cov.: 33

Gnomad AFR AF: 0.532

Gnomad AMI AF: 0.616

Gnomad AMR AF: 0.599

Gnomad ASJ AF: 0.626

Gnomad EAS AF: 0.591

Gnomad SAS AF: 0.506

Gnomad FIN AF: 0.530

Gnomad MID AF: 0.487

Gnomad NFE AF: 0.631

Gnomad OTH AF: 0.571

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

GnomAD4 genome AF: 0.587 AC: 89254 AN: 152030 Hom.: 26459 Cov.: 33 AF XY: 0.583 AC XY: 43289 AN XY: 74306

Gnomad4 AFR AF: 0.531

Gnomad4 AMR AF: 0.599

Gnomad4 ASJ AF: 0.626

Gnomad4 EAS AF: 0.591

Gnomad4 SAS AF: 0.506

Gnomad4 FIN AF: 0.530

Gnomad4 NFE AF: 0.631

Gnomad4 OTH AF: 0.572

Alfa AF: 0.603 Hom.: 3478

Bravo AF: 0.592

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
CADD	Benign	1.1

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs16747; hg19: -;