rs17776120

Variant names:

• chr3-187014891-C-A
• rs17776120
• NM_173216.2:c.-182-23851C>A

Your query was ambiguous. Multiple possible variants found:

• chr3-187014891-C-A
• chr3-187014891-C-G

Variant summary

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

The NM_173216.2(ST6GAL1):​c.-182-23851C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.325 in 152,034 control chromosomes in the GnomAD database, including 8,790 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 (8790 hom., cov: 32)
• Consequence: ST6GAL1 NM_173216.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0390
• 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=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.396 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_173216.2. 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
	ST6GAL1	NM_173216.2	MANE Select	c.-182-23851C>A		intron	N/A	NP_775323.1	P15907-1
	ST6GAL1	NM_173217.2		c.-218-23851C>A		intron	N/A	NP_775324.1	P15907-2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ST6GAL1	ENST00000169298.8	TSL:1 MANE Select	c.-182-23851C>A		intron	N/A	ENSP00000169298.3	P15907-1
	ST6GAL1	ENST00000912781.1		c.-182-23851C>A		intron	N/A	ENSP00000582840.1
	ST6GAL1	ENST00000676633.1		c.-183+18218C>A		intron	N/A	ENSP00000504448.1	P15907-1

Frequencies

GnomAD3 genomes AF: 0.325 AC: 49428 AN: 151916 Hom.: 8784 Cov.: 32

Gnomad AFR AF: 0.179

Gnomad AMI AF: 0.116

Gnomad AMR AF: 0.392

Gnomad ASJ AF: 0.411

Gnomad EAS AF: 0.410

Gnomad SAS AF: 0.404

Gnomad FIN AF: 0.382

Gnomad MID AF: 0.266

Gnomad NFE AF: 0.378

Gnomad OTH AF: 0.310

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

GnomAD4 genome AF: 0.325 AC: 49449 AN: 152034 Hom.: 8790 Cov.: 32 AF XY: 0.327 AC XY: 24308 AN XY: 74282

African (AFR) AF: 0.179 AC: 7436 AN: 41500

American (AMR) AF: 0.393 AC: 6012 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.411 AC: 1426 AN: 3468

East Asian (EAS) AF: 0.411 AC: 2121 AN: 5162

South Asian (SAS) AF: 0.402 AC: 1939 AN: 4818

European-Finnish (FIN) AF: 0.382 AC: 4028 AN: 10544

Middle Eastern (MID) AF: 0.255 AC: 75 AN: 294

European-Non Finnish (NFE) AF: 0.378 AC: 25653 AN: 67948

Other (OTH) AF: 0.309 AC: 653 AN: 2110

Alfa AF: 0.360 Hom.: 32594

Bravo AF: 0.320

Asia WGS AF: 0.402 AC: 1396 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	1.5
DANN	Benign	0.54
PhyloP100		-0.039
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: rs17776120; hg19: chr3-186732679;