8-133458388-T-C

Position:

• chr8-133458388-T-C

Variant summary

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

The NM_173344.3(ST3GAL1):​c.*1376A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.468 in 152,000 control chromosomes in the GnomAD database, including 17,341 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 0.47 (17341 hom., cov: 32)
  • Exomes 𝑓: 0.23 (0 hom.)
• Consequence: ST3GAL1 NM_173344.3 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.555

Genes affected

ST3GAL1 (HGNC:10862): (ST3 beta-galactoside alpha-2,3-sialyltransferase 1) 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 but can be proteolytically processed to a soluble form. Correct glycosylation of the encoded protein may be critical to its sialyltransferase activity. This protein, which is a member of glycosyltransferase family 29, can use the same acceptor substrates as does sialyltransferase 4B. Two transcript variants encoding the same protein have been found for this gene. Other transcript variants may exist, but have not been fully characterized yet. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.603 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ST3GAL1	NM_173344.3	c.*1376A>G		3_prime_UTR_variant	10/10	ENST00000522652.6	NP_775479.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ST3GAL1	ENST00000522652	c.*1376A>G		3_prime_UTR_variant	10/10	1	NM_173344.3	ENSP00000430515.1
ST3GAL1	ENST00000521180	c.*1376A>G		3_prime_UTR_variant	9/9	1		ENSP00000428540.1

Frequencies

GnomAD3 genomes AF: 0.467 AC: 70967 AN: 151860 Hom.: 17302 Cov.: 32

Gnomad AFR AF: 0.609

Gnomad AMI AF: 0.402

Gnomad AMR AF: 0.347

Gnomad ASJ AF: 0.563

Gnomad EAS AF: 0.545

Gnomad SAS AF: 0.437

Gnomad FIN AF: 0.368

Gnomad MID AF: 0.408

Gnomad NFE AF: 0.417

Gnomad OTH AF: 0.440

GnomAD4 exome AF: 0.227 AC: 5 AN: 22 Hom.: 0 Cov.: 0 AF XY: 0.200 AC XY: 2 AN XY: 10

Gnomad4 FIN exome AF: 0.200

Gnomad4 NFE exome AF: 0.375

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome AF: 0.468 AC: 71065 AN: 151978 Hom.: 17341 Cov.: 32 AF XY: 0.461 AC XY: 34213 AN XY: 74286

Gnomad4 AFR AF: 0.609

Gnomad4 AMR AF: 0.347

Gnomad4 ASJ AF: 0.563

Gnomad4 EAS AF: 0.545

Gnomad4 SAS AF: 0.435

Gnomad4 FIN AF: 0.368

Gnomad4 NFE AF: 0.417

Gnomad4 OTH AF: 0.445

Alfa AF: 0.429 Hom.: 19226

Bravo AF: 0.472

Asia WGS AF: 0.502 AC: 1747 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	7.7
DANN	Benign	0.83

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: rs2142306; hg19: chr8-134470631;