1-43750157-C-T

Variant summary

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

The NM_006279.5(ST3GAL3):c.118+13777C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.32 in 152,134 control chromosomes in the GnomAD database, including 9,343 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 0.32 (9343 hom., cov: 32)
• Consequence: ST3GAL3 NM_006279.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.260

Genes affected

ST3GAL3 (HGNC:10866): (ST3 beta-galactoside alpha-2,3-sialyltransferase 3) The protein encoded by this gene is a type II membrane protein that catalyzes the transfer of sialic acid from CMP-sialic acid to galactose-containing substrates. The encoded protein is normally found in the Golgi apparatus but can be proteolytically processed to a soluble form. This protein is a member of glycosyltransferase family 29. Mutations in this gene have been associated with a form of autosomal recessive nonsymdromic cognitive disability as well as infantile epileptic encephalopathy. Multiple transcript variants encoding several different isoforms have been found for this gene. [provided by RefSeq, Jul 2017]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.512 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ST3GAL3	NM_006279.5	c.118+13777C>T		intron_variant		ENST00000347631.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ST3GAL3	ENST00000347631.8	c.118+13777C>T		intron_variant		5	NM_006279.5	A1

Frequencies

GnomAD3 genomes AF: 0.320 AC: 48669 AN: 152014 Hom.: 9341 Cov.: 32

Gnomad AFR AF: 0.106

Gnomad AMI AF: 0.392

Gnomad AMR AF: 0.289

Gnomad ASJ AF: 0.368

Gnomad EAS AF: 0.529

Gnomad SAS AF: 0.396

Gnomad FIN AF: 0.396

Gnomad MID AF: 0.268

Gnomad NFE AF: 0.421

Gnomad OTH AF: 0.319

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

GnomAD4 genome AF: 0.320 AC: 48681 AN: 152134 Hom.: 9343 Cov.: 32 AF XY: 0.321 AC XY: 23835 AN XY: 74352

Gnomad4 AFR AF: 0.106

Gnomad4 AMR AF: 0.289

Gnomad4 ASJ AF: 0.368

Gnomad4 EAS AF: 0.529

Gnomad4 SAS AF: 0.396

Gnomad4 FIN AF: 0.396

Gnomad4 NFE AF: 0.421

Gnomad4 OTH AF: 0.322

Alfa AF: 0.276 Hom.: 1059

Bravo AF: 0.305

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
Cadd	Benign	4.0
Dann	Benign	0.75

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: rs2367725; hg19: chr1-44215828;