2-241817616-T-C

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 4 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001167600.3. 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
	NEU4	NM_001167600.3	MANE Select	c.*568T>C		downstream_gene	N/A	NP_001161072.1	B3KR54
	NEU4	NM_001167599.3		c.*568T>C		downstream_gene	N/A	NP_001161071.1	Q8WWR8-3
	NEU4	NM_080741.4		c.*568T>C		downstream_gene	N/A	NP_542779.2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NEU4	ENST00000407683.6	TSL:2 MANE Select	c.*568T>C		downstream_gene	N/A	ENSP00000385402.1	Q8WWR8-1
	NEU4	ENST00000325935.10	TSL:1	c.*568T>C		downstream_gene	N/A	ENSP00000320318.6	Q8WWR8-3
	NEU4	ENST00000404257.5	TSL:1	c.*568T>C		downstream_gene	N/A	ENSP00000385149.1	Q8WWR8-2

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

African (AFR) AF: 0.531 AC: 22038 AN: 41466

American (AMR) AF: 0.599 AC: 9161 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.626 AC: 2167 AN: 3462

East Asian (EAS) AF: 0.591 AC: 3030 AN: 5126

South Asian (SAS) AF: 0.506 AC: 2435 AN: 4816

European-Finnish (FIN) AF: 0.530 AC: 5607 AN: 10584

Middle Eastern (MID) AF: 0.486 AC: 143 AN: 294

European-Non Finnish (NFE) AF: 0.631 AC: 42903 AN: 67976

Other (OTH) AF: 0.572 AC: 1209 AN: 2112

Alfa AF: 0.603 Hom.: 3478

Bravo AF: 0.592

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
CADD	Benign	1.1
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs16747;