15-92423596-T-G

Position:

• chr15-92423596-T-G

Variant summary

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

The NM_006011.4(ST8SIA2):​c.99-6453T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.425 in 152,170 control chromosomes in the GnomAD database, including 14,932 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 0.43 (14932 hom., cov: 33)
• Consequence: ST8SIA2 NM_006011.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.527

Genes affected

ST8SIA2 (HGNC:10870): (ST8 alpha-N-acetyl-neuraminide alpha-2,8-sialyltransferase 2) The protein encoded by this gene is a type II membrane protein that is thought to catalyze the transfer of sialic acid from CMP-sialic acid to N-linked oligosaccharides and glycoproteins. The encoded protein may be found in the Golgi apparatus and may be involved in the production of polysialic acid, a modulator of the adhesive properties of neural cell adhesion molecule (NCAM1). This protein is a member of glycosyltransferase family 29. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.681 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ST8SIA2	NM_006011.4	c.99-6453T>G		intron_variant		ENST00000268164.8	NP_006002.1
ST8SIA2	NM_001330416.2	c.99-10651T>G		intron_variant			NP_001317345.1
ST8SIA2	XM_017022642.2	c.162-6453T>G		intron_variant			XP_016878131.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ST8SIA2	ENST00000268164.8	c.99-6453T>G		intron_variant		1	NM_006011.4	ENSP00000268164	P1
ST8SIA2	ENST00000539113.5	c.99-10651T>G		intron_variant		1		ENSP00000437382
ST8SIA2	ENST00000555434.1	c.99-6453T>G		intron_variant		5		ENSP00000450851

Frequencies

GnomAD3 genomes AF: 0.426 AC: 64732 AN: 152052 Hom.: 14924 Cov.: 33

Gnomad AFR AF: 0.255

Gnomad AMI AF: 0.362

Gnomad AMR AF: 0.519

Gnomad ASJ AF: 0.530

Gnomad EAS AF: 0.699

Gnomad SAS AF: 0.488

Gnomad FIN AF: 0.415

Gnomad MID AF: 0.506

Gnomad NFE AF: 0.480

Gnomad OTH AF: 0.431

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

GnomAD4 genome AF: 0.425 AC: 64747 AN: 152170 Hom.: 14932 Cov.: 33 AF XY: 0.431 AC XY: 32068 AN XY: 74410

Gnomad4 AFR AF: 0.254

Gnomad4 AMR AF: 0.520

Gnomad4 ASJ AF: 0.530

Gnomad4 EAS AF: 0.700

Gnomad4 SAS AF: 0.488

Gnomad4 FIN AF: 0.415

Gnomad4 NFE AF: 0.480

Gnomad4 OTH AF: 0.426

Alfa AF: 0.461 Hom.: 4630

Bravo AF: 0.426

Asia WGS AF: 0.530 AC: 1836 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.86
DANN	Benign	0.50

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: rs11074070; hg19: chr15-92966826;