rs11710456

Variant names:

• chr3-187008099-G-A
• rs11710456
• NM_173216.2:c.-182-30643G>A

Variant summary

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

The NM_173216.2(ST6GAL1):​c.-182-30643G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.326 in 151,890 control chromosomes in the GnomAD database, including 8,259 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 0.33 (8259 hom., cov: 32)
• Consequence: ST6GAL1 NM_173216.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.28
• Publications: 15 publications found

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

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.422 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ST6GAL1	NM_173216.2	c.-182-30643G>A		intron_variant	Intron 2 of 7	ENST00000169298.8	NP_775323.1
ST6GAL1	NM_173217.2	c.-218-30643G>A		intron_variant	Intron 2 of 6		NP_775324.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ST6GAL1	ENST00000169298.8	c.-182-30643G>A		intron_variant	Intron 2 of 7	1	NM_173216.2	ENSP00000169298.3

Frequencies

GnomAD3 genomes AF: 0.326 AC: 49512 AN: 151772 Hom.: 8251 Cov.: 32

Gnomad AFR AF: 0.378

Gnomad AMI AF: 0.124

Gnomad AMR AF: 0.339

Gnomad ASJ AF: 0.348

Gnomad EAS AF: 0.307

Gnomad SAS AF: 0.440

Gnomad FIN AF: 0.361

Gnomad MID AF: 0.237

Gnomad NFE AF: 0.283

Gnomad OTH AF: 0.296

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

GnomAD4 genome AF: 0.326 AC: 49550 AN: 151890 Hom.: 8259 Cov.: 32 AF XY: 0.332 AC XY: 24639 AN XY: 74230

African (AFR) AF: 0.377 AC: 15635 AN: 41430

American (AMR) AF: 0.339 AC: 5180 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.348 AC: 1206 AN: 3470

East Asian (EAS) AF: 0.308 AC: 1591 AN: 5172

South Asian (SAS) AF: 0.438 AC: 2114 AN: 4826

European-Finnish (FIN) AF: 0.361 AC: 3787 AN: 10488

Middle Eastern (MID) AF: 0.228 AC: 67 AN: 294

European-Non Finnish (NFE) AF: 0.283 AC: 19229 AN: 67940

Other (OTH) AF: 0.299 AC: 628 AN: 2100

Alfa AF: 0.296 Hom.: 9709

Bravo AF: 0.320

Asia WGS AF: 0.386 AC: 1341 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.33
DANN	Benign	0.48
PhyloP100		-1.3
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: rs11710456; hg19: chr3-186725887;