chr2-241817616-T-A

Variant names:

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

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_001167600.3(NEU4):​c.*568T>A variant causes a downstream gene change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (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: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (Cadd=0.958).

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>A		downstream_gene	N/A	NP_001161072.1	B3KR54
	NEU4	NM_001167599.3		c.*568T>A		downstream_gene	N/A	NP_001161071.1	Q8WWR8-3
	NEU4	NM_080741.4		c.*568T>A		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>A		downstream_gene	N/A	ENSP00000385402.1	Q8WWR8-1
	NEU4	ENST00000325935.10	TSL:1	c.*568T>A		downstream_gene	N/A	ENSP00000320318.6	Q8WWR8-3
	NEU4	ENST00000404257.5	TSL:1	c.*568T>A		downstream_gene	N/A	ENSP00000385149.1	Q8WWR8-2

Frequencies

GnomAD3 genomes Cov.: 33

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

GnomAD4 genome Cov.: 33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
CADD	Benign	0.96
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;