chr15-92397670-T-C

Variant names:

• chr15-92397670-T-C
• rs8025225
• NM_006011.4:c.98+3508T>C

Variant summary

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

The NM_006011.4(ST8SIA2):​c.98+3508T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.444 in 151,994 control chromosomes in the GnomAD database, including 15,341 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 (15341 hom., cov: 33)
• Consequence: ST8SIA2 NM_006011.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.435

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=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.485 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ST8SIA2	NM_006011.4	c.98+3508T>C		intron_variant	Intron 1 of 5	ENST00000268164.8	NP_006002.1
ST8SIA2	NM_001330416.2	c.98+3508T>C		intron_variant	Intron 1 of 4		NP_001317345.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ST8SIA2	ENST00000268164.8	c.98+3508T>C		intron_variant	Intron 1 of 5	1	NM_006011.4	ENSP00000268164.3
ST8SIA2	ENST00000539113.5	c.98+3508T>C		intron_variant	Intron 1 of 4	1		ENSP00000437382.1
ST8SIA2	ENST00000555434.1	c.98+3508T>C		intron_variant	Intron 1 of 4	5		ENSP00000450851.1

Frequencies

GnomAD3 genomes AF: 0.444 AC: 67420 AN: 151876 Hom.: 15339 Cov.: 33

Gnomad AFR AF: 0.368

Gnomad AMI AF: 0.412

Gnomad AMR AF: 0.436

Gnomad ASJ AF: 0.486

Gnomad EAS AF: 0.375

Gnomad SAS AF: 0.374

Gnomad FIN AF: 0.512

Gnomad MID AF: 0.528

Gnomad NFE AF: 0.489

Gnomad OTH AF: 0.460

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

GnomAD4 genome AF: 0.444 AC: 67450 AN: 151994 Hom.: 15341 Cov.: 33 AF XY: 0.445 AC XY: 33045 AN XY: 74286

Gnomad4 AFR AF: 0.367

Gnomad4 AMR AF: 0.436

Gnomad4 ASJ AF: 0.486

Gnomad4 EAS AF: 0.377

Gnomad4 SAS AF: 0.373

Gnomad4 FIN AF: 0.512

Gnomad4 NFE AF: 0.489

Gnomad4 OTH AF: 0.454

Alfa AF: 0.481 Hom.: 18003

Bravo AF: 0.434

Asia WGS AF: 0.361 AC: 1253 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	9.3
DANN	Benign	0.63

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: rs8025225; hg19: chr15-92940900;