rs3784735

Positions:

• chr15-92432099-A-C
• chr15-92432099-A-T

Variant summary

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

The NM_006011.4(ST8SIA2):​c.161+1988A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.441 in 151,914 control chromosomes in the GnomAD database, including 16,073 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 0.44 (16073 hom., cov: 31)
• Consequence: ST8SIA2 NM_006011.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0900

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=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.682 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ST8SIA2	NM_006011.4	c.161+1988A>C		intron_variant		ENST00000268164.8	NP_006002.1
ST8SIA2	NM_001330416.2	c.99-2148A>C		intron_variant			NP_001317345.1
ST8SIA2	XM_017022642.2	c.224+1988A>C		intron_variant			XP_016878131.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ST8SIA2	ENST00000268164.8	c.161+1988A>C		intron_variant		1	NM_006011.4	ENSP00000268164.3
ST8SIA2	ENST00000539113.5	c.99-2148A>C		intron_variant		1		ENSP00000437382.1
ST8SIA2	ENST00000555434.1	c.161+1988A>C		intron_variant		5		ENSP00000450851.1

Frequencies

GnomAD3 genomes AF: 0.441 AC: 66928 AN: 151796 Hom.: 16066 Cov.: 31

Gnomad AFR AF: 0.251

Gnomad AMI AF: 0.363

Gnomad AMR AF: 0.536

Gnomad ASJ AF: 0.550

Gnomad EAS AF: 0.701

Gnomad SAS AF: 0.500

Gnomad FIN AF: 0.471

Gnomad MID AF: 0.478

Gnomad NFE AF: 0.502

Gnomad OTH AF: 0.443

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

GnomAD4 genome AF: 0.441 AC: 66949 AN: 151914 Hom.: 16073 Cov.: 31 AF XY: 0.447 AC XY: 33226 AN XY: 74258

Gnomad4 AFR AF: 0.250

Gnomad4 AMR AF: 0.536

Gnomad4 ASJ AF: 0.550

Gnomad4 EAS AF: 0.701

Gnomad4 SAS AF: 0.500

Gnomad4 FIN AF: 0.471

Gnomad4 NFE AF: 0.502

Gnomad4 OTH AF: 0.439

Alfa AF: 0.478 Hom.: 16365

Bravo AF: 0.436

Asia WGS AF: 0.539 AC: 1870 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.6
DANN	Benign	0.74

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: rs3784735; hg19: chr15-92975329;