rs17160771

Positions:

• chr5-100875122-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.503+11221A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.129 in 152,190 control chromosomes in the GnomAD database, including 2,345 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 0.13 (2345 hom., cov: 32)
• Consequence: ST8SIA4 NM_005668.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.121

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=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.298 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ST8SIA4	NM_005668.6	c.503+11221A>G		intron_variant		ENST00000231461.10	NP_005659.1
ST8SIA4	XM_005272078.4	c.503+11221A>G		intron_variant			XP_005272135.1
ST8SIA4	XM_011543630.3	c.503+11221A>G		intron_variant			XP_011541932.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ST8SIA4	ENST00000231461.10	c.503+11221A>G		intron_variant		1	NM_005668.6	ENSP00000231461.4

Frequencies

GnomAD3 genomes AF: 0.128 AC: 19535 AN: 152072 Hom.: 2331 Cov.: 32

Gnomad AFR AF: 0.302

Gnomad AMI AF: 0.0669

Gnomad AMR AF: 0.190

Gnomad ASJ AF: 0.0605

Gnomad EAS AF: 0.00810

Gnomad SAS AF: 0.0232

Gnomad FIN AF: 0.0412

Gnomad MID AF: 0.0380

Gnomad NFE AF: 0.0441

Gnomad OTH AF: 0.119

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

GnomAD4 genome AF: 0.129 AC: 19592 AN: 152190 Hom.: 2345 Cov.: 32 AF XY: 0.126 AC XY: 9396 AN XY: 74414

Gnomad4 AFR AF: 0.302

Gnomad4 AMR AF: 0.191

Gnomad4 ASJ AF: 0.0605

Gnomad4 EAS AF: 0.00792

Gnomad4 SAS AF: 0.0236

Gnomad4 FIN AF: 0.0412

Gnomad4 NFE AF: 0.0441

Gnomad4 OTH AF: 0.118

Alfa AF: 0.0646 Hom.: 333

Bravo AF: 0.151

Asia WGS AF: 0.0410 AC: 143 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	5.2
DANN	Benign	0.62

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: rs17160771; hg19: chr5-100210826;