rs410076

Variant names:

• chr1-76535946-G-A
• rs410076
• NM_152996.4:c.624-91506G>A

Variant summary

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

The NM_152996.4(ST6GALNAC3):​c.624-91506G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.847 in 152,106 control chromosomes in the GnomAD database, including 54,630 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 0.85 (54630 hom., cov: 32)
• Consequence: ST6GALNAC3 NM_152996.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0260
• 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=-0.8).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.859 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ST6GALNAC3	NM_152996.4	c.624-91506G>A		intron_variant	Intron 3 of 4	ENST00000328299.4	NP_694541.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ST6GALNAC3	ENST00000328299.4	c.624-91506G>A		intron_variant	Intron 3 of 4	1	NM_152996.4	ENSP00000329214.3
ST6GALNAC3	ENST00000464140.1	n.498-40900G>A		intron_variant	Intron 2 of 2	1

Frequencies

GnomAD3 genomes AF: 0.847 AC: 128753 AN: 151986 Hom.: 54592 Cov.: 32

Gnomad AFR AF: 0.848

Gnomad AMI AF: 0.940

Gnomad AMR AF: 0.809

Gnomad ASJ AF: 0.821

Gnomad EAS AF: 0.760

Gnomad SAS AF: 0.816

Gnomad FIN AF: 0.835

Gnomad MID AF: 0.918

Gnomad NFE AF: 0.865

Gnomad OTH AF: 0.863

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

GnomAD4 genome AF: 0.847 AC: 128834 AN: 152106 Hom.: 54630 Cov.: 32 AF XY: 0.843 AC XY: 62728 AN XY: 74370

African (AFR) AF: 0.847 AC: 35160 AN: 41488

American (AMR) AF: 0.809 AC: 12355 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.821 AC: 2849 AN: 3470

East Asian (EAS) AF: 0.761 AC: 3920 AN: 5154

South Asian (SAS) AF: 0.817 AC: 3944 AN: 4830

European-Finnish (FIN) AF: 0.835 AC: 8831 AN: 10576

Middle Eastern (MID) AF: 0.925 AC: 272 AN: 294

European-Non Finnish (NFE) AF: 0.865 AC: 58820 AN: 68002

Other (OTH) AF: 0.865 AC: 1826 AN: 2112

Alfa AF: 0.854 Hom.: 41651

Bravo AF: 0.846

Asia WGS AF: 0.769 AC: 2664 AN: 3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	12
DANN	Benign	0.61
PhyloP100		-0.026
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: rs410076; hg19: chr1-77001631;