5-100829413-T-C

Variant names:

• chr5-100829413-T-C
• rs2548278
• NM_005668.6:c.798-17284A>G

Variant summary

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

The NM_005668.6(ST8SIA4):​c.798-17284A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.578 in 152,046 control chromosomes in the GnomAD database, including 26,150 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 0.58 (26150 hom., cov: 32)
• Consequence: ST8SIA4 NM_005668.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.170
• Publications: 10 publications found

Genes affected

ST8SIA4 (HGNC:10871): (ST8 alpha-N-acetyl-neuraminide alpha-2,8-sialyltransferase 4) The protein encoded by this gene catalyzes the polycondensation of alpha-2,8-linked sialic acid required for the synthesis of polysialic acid, a modulator of the adhesive properties of neural cell adhesion molecule (NCAM1). The encoded protein, which is a member of glycosyltransferase family 29, is a type II membrane protein that may be present in the Golgi apparatus. Two transcript variants encoding different isoforms have been found for this gene. [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=-0.85).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.716 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_005668.6. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ST8SIA4	NM_005668.6	MANE Select	c.798-17284A>G		intron	N/A	NP_005659.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ST8SIA4	ENST00000231461.10	TSL:1 MANE Select	c.798-17284A>G		intron	N/A	ENSP00000231461.4

Frequencies

GnomAD3 genomes AF: 0.578 AC: 87832 AN: 151928 Hom.: 26144 Cov.: 32

Gnomad AFR AF: 0.441

Gnomad AMI AF: 0.678

Gnomad AMR AF: 0.539

Gnomad ASJ AF: 0.713

Gnomad EAS AF: 0.707

Gnomad SAS AF: 0.736

Gnomad FIN AF: 0.627

Gnomad MID AF: 0.653

Gnomad NFE AF: 0.633

Gnomad OTH AF: 0.591

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

GnomAD4 genome AF: 0.578 AC: 87853 AN: 152046 Hom.: 26150 Cov.: 32 AF XY: 0.579 AC XY: 43035 AN XY: 74330

African (AFR) AF: 0.441 AC: 18266 AN: 41458

American (AMR) AF: 0.539 AC: 8224 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.713 AC: 2477 AN: 3472

East Asian (EAS) AF: 0.707 AC: 3657 AN: 5172

South Asian (SAS) AF: 0.736 AC: 3541 AN: 4812

European-Finnish (FIN) AF: 0.627 AC: 6624 AN: 10564

Middle Eastern (MID) AF: 0.644 AC: 188 AN: 292

European-Non Finnish (NFE) AF: 0.633 AC: 43005 AN: 67986

Other (OTH) AF: 0.594 AC: 1254 AN: 2110

Alfa AF: 0.616 Hom.: 92561

Bravo AF: 0.564

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	5.3
DANN	Benign	0.84
PhyloP100		0.17
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs2548278; hg19: chr5-100165117;