rs16861471

chr3-187006889-A-C

Variant summary

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

The NM_173216.2(ST6GAL1):c.-182-31853A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0788 in 152,254 control chromosomes in the GnomAD database, including 556 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 0.079 (556 hom., cov: 33)
• Consequence: ST6GAL1 NM_173216.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.117

Genes affected

ST6GAL1 (HGNC:10860): (ST6 beta-galactoside alpha-2,6-sialyltransferase 1) This gene encodes a member of glycosyltransferase family 29. The encoded protein is a type II membrane protein that catalyzes the transfer of sialic acid from CMP-sialic acid to galactose-containing substrates. The protein, which is normally found in the Golgi but can be proteolytically processed to a soluble form, is involved in the generation of the cell-surface carbohydrate determinants and differentiation antigens HB-6, CD75, and CD76. This gene has been incorrectly referred to as CD75. Alternative splicing results in multiple transcript variants. [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 (AFR) allele frequency at 95% confidence interval = 0.124 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ST6GAL1	NM_173216.2	c.-182-31853A>C		intron_variant		ENST00000169298.8
ST6GAL1	NM_173217.2	c.-218-31853A>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ST6GAL1	ENST00000169298.8	c.-182-31853A>C		intron_variant		1	NM_173216.2	P1

Frequencies

GnomAD3 genomes AF: 0.0789 AC: 11997 AN: 152136 Hom.: 555 Cov.: 33

Gnomad AFR AF: 0.127

Gnomad AMI AF: 0.117

Gnomad AMR AF: 0.0650

Gnomad ASJ AF: 0.120

Gnomad EAS AF: 0.000192

Gnomad SAS AF: 0.0135

Gnomad FIN AF: 0.0444

Gnomad MID AF: 0.127

Gnomad NFE AF: 0.0652

Gnomad OTH AF: 0.0996

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

GnomAD4 genome AF: 0.0788 AC: 12000 AN: 152254 Hom.: 556 Cov.: 33 AF XY: 0.0756 AC XY: 5632 AN XY: 74460

Gnomad4 AFR AF: 0.127

Gnomad4 AMR AF: 0.0648

Gnomad4 ASJ AF: 0.120

Gnomad4 EAS AF: 0.000193

Gnomad4 SAS AF: 0.0133

Gnomad4 FIN AF: 0.0444

Gnomad4 NFE AF: 0.0652

Gnomad4 OTH AF: 0.0981

Alfa AF: 0.0717 Hom.: 67

Bravo AF: 0.0861

Asia WGS AF: 0.0200 AC: 68 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
Cadd	Benign	3.2
Dann	Benign	0.88

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: rs16861471; hg19: chr3-186724677;