5-100829413-T-C

Position:

• chr5-100829413-T-C

Variant summary

Our verdict is Benign. Variant got -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

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

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ST8SIA4	NM_005668.6	c.798-17284A>G		intron_variant		ENST00000231461.10	NP_005659.1
ST8SIA4	XM_011543630.3	c.504-17284A>G		intron_variant			XP_011541932.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ST8SIA4	ENST00000231461.10	c.798-17284A>G		intron_variant		1	NM_005668.6	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

Gnomad4 AFR AF: 0.441

Gnomad4 AMR AF: 0.539

Gnomad4 ASJ AF: 0.713

Gnomad4 EAS AF: 0.707

Gnomad4 SAS AF: 0.736

Gnomad4 FIN AF: 0.627

Gnomad4 NFE AF: 0.633

Gnomad4 OTH AF: 0.594

Alfa AF: 0.630 Hom.: 59675

Bravo AF: 0.564

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	5.3
DANN	Benign	0.84

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

Publications

LitVar

Other links and lift over

dbSNP: rs2548278; hg19: chr5-100165117;