rs289681

chr1-76103108-T-G

Variant summary

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

The NM_152996.4(ST6GALNAC3):c.18+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_152996.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0960

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

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ST6GALNAC3	NM_152996.4	c.18+28224T>G		intron_variant		ENST00000328299.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ST6GALNAC3	ENST00000328299.4	c.18+28224T>G		intron_variant		1	NM_152996.4	P1

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

Gnomad4 AFR AF: 0.150

Gnomad4 AMR AF: 0.146

Gnomad4 ASJ AF: 0.145

Gnomad4 EAS AF: 0.0266

Gnomad4 SAS AF: 0.130

Gnomad4 FIN AF: 0.272

Gnomad4 NFE AF: 0.191

Gnomad4 OTH AF: 0.159

Alfa AF: 0.173 Hom.: 455

Bravo AF: 0.155

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	1.4
Dann	Benign	0.49

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: rs289681; hg19: chr1-76568793;