1-76306643-T-C

Variant summary

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

The NM_152996.4(ST6GALNAC3):c.19-7162T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.752 in 150,204 control chromosomes in the GnomAD database, including 43,443 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 0.75 (43443 hom., cov: 26)
• Consequence: ST6GALNAC3 NM_152996.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.186

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=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.835 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ST6GALNAC3	NM_152996.4	c.19-7162T>C		intron_variant		ENST00000328299.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ST6GALNAC3	ENST00000328299.4	c.19-7162T>C		intron_variant		1	NM_152996.4	P1

Frequencies

GnomAD3 genomes AF: 0.752 AC: 112879 AN: 150094 Hom.: 43413 Cov.: 26

Gnomad AFR AF: 0.570

Gnomad AMI AF: 0.827

Gnomad AMR AF: 0.782

Gnomad ASJ AF: 0.744

Gnomad EAS AF: 0.734

Gnomad SAS AF: 0.824

Gnomad FIN AF: 0.822

Gnomad MID AF: 0.721

Gnomad NFE AF: 0.841

Gnomad OTH AF: 0.744

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

GnomAD4 genome AF: 0.752 AC: 112954 AN: 150204 Hom.: 43443 Cov.: 26 AF XY: 0.752 AC XY: 55077 AN XY: 73198

Gnomad4 AFR AF: 0.571

Gnomad4 AMR AF: 0.782

Gnomad4 ASJ AF: 0.744

Gnomad4 EAS AF: 0.734

Gnomad4 SAS AF: 0.823

Gnomad4 FIN AF: 0.822

Gnomad4 NFE AF: 0.841

Gnomad4 OTH AF: 0.745

Alfa AF: 0.819 Hom.: 113858

Bravo AF: 0.735

Asia WGS AF: 0.798 AC: 2771 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	3.7
Dann	Benign	0.75

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: rs10873876; hg19: chr1-76772328;