NM_005668.6:c.503+11221A>G

Variant names:

• chr5-100875122-T-C
• rs17160771
• NM_005668.6:c.503+11221A>G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 3 publications found

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

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
ST8SIA4	NM_005668.6	c.503+11221A>G		intron_variant	Intron 3 of 4	ENST00000231461.10	NP_005659.1
ST8SIA4	XM_005272078.4	c.503+11221A>G		intron_variant	Intron 3 of 4		XP_005272135.1
ST8SIA4	XM_011543630.3	c.503+11221A>G		intron_variant	Intron 3 of 3		XP_011541932.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ST8SIA4	ENST00000231461.10	c.503+11221A>G		intron_variant	Intron 3 of 4	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

African (AFR) AF: 0.302 AC: 12553 AN: 41502

American (AMR) AF: 0.191 AC: 2917 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.0605 AC: 210 AN: 3472

East Asian (EAS) AF: 0.00792 AC: 41 AN: 5174

South Asian (SAS) AF: 0.0236 AC: 114 AN: 4826

European-Finnish (FIN) AF: 0.0412 AC: 438 AN: 10624

Middle Eastern (MID) AF: 0.0408 AC: 12 AN: 294

European-Non Finnish (NFE) AF: 0.0441 AC: 2998 AN: 68012

Other (OTH) AF: 0.118 AC: 248 AN: 2110

Alfa AF: 0.0665 Hom.: 390

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
PhyloP100		-0.12
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs17160771; hg19: chr5-100210826;