rs289681

Variant names:

• chr1-76103108-T-G
• rs289681
• NM_152996.4:c.18+28224T>G

Variant summary

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

The NM_001349111.2(ST6GALNAC3):​c.-54+28224T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.173 in 141,744 control chromosomes in the GnomAD database, including 2,171 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 0.17 (2171 hom., cov: 30)
• Consequence: ST6GALNAC3 NM_001349111.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0960
• Publications: 1 publications found

Genes affected

ST6GALNAC3 (HGNC:19343): (ST6 N-acetylgalactosaminide alpha-2,6-sialyltransferase 3) ST6GALNAC3 belongs to a family of sialyltransferases that transfer sialic acids from CMP-sialic acid to terminal positions of carbohydrate groups in glycoproteins and glycolipids (Lee et al., 1999 [PubMed 10207017]).[supplied by OMIM, Mar 2008]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.188 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001349111.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ST6GALNAC3	NM_152996.4	MANE Select	c.18+28224T>G		intron	N/A	NP_694541.2
	ST6GALNAC3	NM_001349111.2		c.-54+28224T>G		intron	N/A	NP_001336040.1
	ST6GALNAC3	NM_001349107.2		c.18+28224T>G		intron	N/A	NP_001336036.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ST6GALNAC3	ENST00000328299.4	TSL:1 MANE Select	c.18+28224T>G		intron	N/A	ENSP00000329214.3

Frequencies

GnomAD3 genomes AF: 0.173 AC: 24491 AN: 141688 Hom.: 2172 Cov.: 30

Gnomad AFR AF: 0.149

Gnomad AMI AF: 0.225

Gnomad AMR AF: 0.146

Gnomad ASJ AF: 0.145

Gnomad EAS AF: 0.0263

Gnomad SAS AF: 0.130

Gnomad FIN AF: 0.272

Gnomad MID AF: 0.132

Gnomad NFE AF: 0.191

Gnomad OTH AF: 0.161

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

GnomAD4 genome AF: 0.173 AC: 24495 AN: 141744 Hom.: 2171 Cov.: 30 AF XY: 0.176 AC XY: 12128 AN XY: 69040

African (AFR) AF: 0.150 AC: 5370 AN: 35906

American (AMR) AF: 0.146 AC: 1962 AN: 13416

Ashkenazi Jewish (ASJ) AF: 0.145 AC: 485 AN: 3342

East Asian (EAS) AF: 0.0266 AC: 128 AN: 4810

South Asian (SAS) AF: 0.130 AC: 603 AN: 4640

European-Finnish (FIN) AF: 0.272 AC: 2592 AN: 9518

Middle Eastern (MID) AF: 0.126 AC: 35 AN: 278

European-Non Finnish (NFE) AF: 0.191 AC: 12808 AN: 66986

Other (OTH) AF: 0.159 AC: 308 AN: 1942

Alfa AF: 0.185 Hom.: 795

Bravo AF: 0.155

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.4
DANN	Benign	0.49
PhyloP100		0.096
Mutation Taster		=7/93	disease causing (long InDel)

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: rs289681; hg19: chr1-76568793;