NM_001323368.2:c.335+4202G>A

Variant names:

• chr3-98778185-G-A
• rs3755576
• NM_001323368.2:c.335+4202G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001323368.2(ST3GAL6):​c.335+4202G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.412 in 152,020 control chromosomes in the GnomAD database, including 13,085 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 0.41 (13085 hom., cov: 32)
• Consequence: ST3GAL6 NM_001323368.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.607
• Publications: 3 publications found

Genes affected

ST3GAL6 (HGNC:18080): (ST3 beta-galactoside alpha-2,3-sialyltransferase 6) The protein encoded by this gene is a member of the sialyltransferase family. Members of this family are enzymes that transfer sialic acid from the activated cytidine 5'-monophospho-N-acetylneuraminic acid to terminal positions on sialylated glycolipids (gangliosides) or to the N- or O-linked sugar chains of glycoproteins. This protein has high specificity for neolactotetraosylceramide and neolactohexaosylceramide as glycolipid substrates and may contribute to the formation of selectin ligands and sialyl Lewis X, a carbohydrate important for cell-to-cell recognition and a blood group antigen. [provided by RefSeq, Apr 2016]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.445 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001323368.2. 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
	ST3GAL6	NM_001323368.2	MANE Select	c.335+4202G>A		intron	N/A	NP_001310297.1	Q9Y274-1
	ST3GAL6	NM_001271145.2		c.494+4202G>A		intron	N/A	NP_001258074.1	A0A087WXB8
	ST3GAL6	NM_001271146.2		c.335+4202G>A		intron	N/A	NP_001258075.1	Q9Y274-1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ST3GAL6	ENST00000483910.6	TSL:1 MANE Select	c.335+4202G>A		intron	N/A	ENSP00000417376.1	Q9Y274-1
	ST3GAL6	ENST00000394162.5	TSL:1	c.335+4202G>A		intron	N/A	ENSP00000377717.1	Q9Y274-1
	ST3GAL6	ENST00000613264.5	TSL:1	c.335+4202G>A		intron	N/A	ENSP00000480884.2	Q9Y274-1

Frequencies

GnomAD3 genomes AF: 0.412 AC: 62650 AN: 151902 Hom.: 13068 Cov.: 32

Gnomad AFR AF: 0.393

Gnomad AMI AF: 0.329

Gnomad AMR AF: 0.374

Gnomad ASJ AF: 0.413

Gnomad EAS AF: 0.218

Gnomad SAS AF: 0.356

Gnomad FIN AF: 0.437

Gnomad MID AF: 0.376

Gnomad NFE AF: 0.449

Gnomad OTH AF: 0.411

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

GnomAD4 genome AF: 0.412 AC: 62699 AN: 152020 Hom.: 13085 Cov.: 32 AF XY: 0.410 AC XY: 30488 AN XY: 74300

African (AFR) AF: 0.393 AC: 16315 AN: 41470

American (AMR) AF: 0.373 AC: 5708 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.413 AC: 1434 AN: 3470

East Asian (EAS) AF: 0.218 AC: 1127 AN: 5170

South Asian (SAS) AF: 0.357 AC: 1716 AN: 4810

European-Finnish (FIN) AF: 0.437 AC: 4613 AN: 10552

Middle Eastern (MID) AF: 0.387 AC: 113 AN: 292

European-Non Finnish (NFE) AF: 0.449 AC: 30513 AN: 67952

Other (OTH) AF: 0.408 AC: 860 AN: 2108

Alfa AF: 0.419 Hom.: 2146

Bravo AF: 0.403

Asia WGS AF: 0.270 AC: 939 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	3.0
DANN	Benign	0.31
PhyloP100		0.61
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: rs3755576; hg19: chr3-98497029;