18-57360295-C-T

Position:

• chr18-57360295-C-T

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000324000.4(ST8SIA3):​c.*18C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.198 in 1,602,964 control chromosomes in the GnomAD database, including 37,294 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 0.26 (6146 hom., cov: 33)
  • Exomes 𝑓: 0.19 (31148 hom.)
• Consequence: ST8SIA3 ENST00000324000.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.91

Genes affected

ST8SIA3 (HGNC:14269): (ST8 alpha-N-acetyl-neuraminide alpha-2,8-sialyltransferase 3) Enables alpha-N-acetylneuraminate alpha-2,8-sialyltransferase activity and identical protein binding activity. Involved in several processes, including ganglioside biosynthetic process; glycoprotein metabolic process; and protein sialylation. Predicted to be located in Golgi membrane. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.45).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.495 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ST8SIA3	NM_015879.3	c.*18C>T		3_prime_UTR_variant	4/4	ENST00000324000.4	NP_056963.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ST8SIA3	ENST00000324000.4	c.*18C>T		3_prime_UTR_variant	4/4	1	NM_015879.3	ENSP00000320431	P1
ST8SIA3	ENST00000586360.1	c.319+2825C>T		intron_variant		3		ENSP00000467752

Frequencies

GnomAD3 genomes AF: 0.260 AC: 39490 AN: 151968 Hom.: 6130 Cov.: 33

Gnomad AFR AF: 0.395

Gnomad AMI AF: 0.308

Gnomad AMR AF: 0.281

Gnomad ASJ AF: 0.123

Gnomad EAS AF: 0.511

Gnomad SAS AF: 0.291

Gnomad FIN AF: 0.225

Gnomad MID AF: 0.130

Gnomad NFE AF: 0.165

Gnomad OTH AF: 0.221

GnomAD3 exomes AF: 0.245 AC: 60306 AN: 245758 Hom.: 8744 AF XY: 0.237 AC XY: 31564 AN XY: 132922

Gnomad AFR exome AF: 0.391

Gnomad AMR exome AF: 0.313

Gnomad ASJ exome AF: 0.127

Gnomad EAS exome AF: 0.509

Gnomad SAS exome AF: 0.282

Gnomad FIN exome AF: 0.226

Gnomad NFE exome AF: 0.167

Gnomad OTH exome AF: 0.204

GnomAD4 exome AF: 0.192 AC: 278014 AN: 1450878 Hom.: 31148 Cov.: 34 AF XY: 0.193 AC XY: 138704 AN XY: 720208

Gnomad4 AFR exome AF: 0.397

Gnomad4 AMR exome AF: 0.309

Gnomad4 ASJ exome AF: 0.129

Gnomad4 EAS exome AF: 0.519

Gnomad4 SAS exome AF: 0.280

Gnomad4 FIN exome AF: 0.225

Gnomad4 NFE exome AF: 0.162

Gnomad4 OTH exome AF: 0.204

GnomAD4 genome AF: 0.260 AC: 39563 AN: 152086 Hom.: 6146 Cov.: 33 AF XY: 0.266 AC XY: 19746 AN XY: 74344

Gnomad4 AFR AF: 0.395

Gnomad4 AMR AF: 0.281

Gnomad4 ASJ AF: 0.123

Gnomad4 EAS AF: 0.511

Gnomad4 SAS AF: 0.290

Gnomad4 FIN AF: 0.225

Gnomad4 NFE AF: 0.165

Gnomad4 OTH AF: 0.225

Alfa AF: 0.182 Hom.: 3224

Bravo AF: 0.269

Asia WGS AF: 0.399 AC: 1385 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.45
CADD	Benign	15
DANN	Benign	0.91

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: rs739692; hg19: chr18-55027526; COSMIC: COSV60655713; COSMIC: COSV60655713;