8-133458388-T-C

Variant names:

• chr8-133458388-T-C
• rs2142306
• NM_173344.3:c.*1376A>G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 9 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_173344.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ST3GAL1	NM_173344.3	MANE Select	c.*1376A>G		3_prime_UTR	Exon 10 of 10	NP_775479.1
	ST3GAL1	NM_003033.4		c.*1376A>G		3_prime_UTR	Exon 9 of 9	NP_003024.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ST3GAL1	ENST00000522652.6	TSL:1 MANE Select	c.*1376A>G		3_prime_UTR	Exon 10 of 10	ENSP00000430515.1
	ST3GAL1	ENST00000521180.5	TSL:1	c.*1376A>G		3_prime_UTR	Exon 9 of 9	ENSP00000428540.1
	ST3GAL1	ENST00000941228.1		c.*1376A>G		3_prime_UTR	Exon 12 of 12	ENSP00000611287.1

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

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.200 AC: 2 AN: 10

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.375 AC: 3 AN: 8

Other (OTH) AF: 0.00 AC: 0 AN: 4

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

African (AFR) AF: 0.609 AC: 25247 AN: 41428

American (AMR) AF: 0.347 AC: 5300 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.563 AC: 1951 AN: 3464

East Asian (EAS) AF: 0.545 AC: 2816 AN: 5168

South Asian (SAS) AF: 0.435 AC: 2091 AN: 4802

European-Finnish (FIN) AF: 0.368 AC: 3885 AN: 10556

Middle Eastern (MID) AF: 0.418 AC: 123 AN: 294

European-Non Finnish (NFE) AF: 0.417 AC: 28346 AN: 67966

Other (OTH) AF: 0.445 AC: 939 AN: 2112

Alfa AF: 0.433 Hom.: 24762

Bravo AF: 0.472

Asia WGS AF: 0.502 AC: 1747 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	7.7
DANN	Benign	0.83
PhyloP100		0.56
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: rs2142306; hg19: chr8-134470631;