rs1251575

Variant names:

• chr1-76092099-A-G
• rs1251575
• NM_152996.4:c.18+17215A>G

Variant summary

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

Score: -12 - Benign

-12

BP4_StrongBA1

The NM_152996.4(ST6GALNAC3):​c.18+17215A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.373 in 151,928 control chromosomes in the GnomAD database, including 12,175 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 0.37 (12175 hom., cov: 32)
• Consequence: ST6GALNAC3 NM_152996.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.659
• Publications: 3 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=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.586 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ST6GALNAC3	NM_152996.4	c.18+17215A>G		intron_variant	Intron 1 of 4	ENST00000328299.4	NP_694541.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ST6GALNAC3	ENST00000328299.4	c.18+17215A>G		intron_variant	Intron 1 of 4	1	NM_152996.4	ENSP00000329214.3

Frequencies

GnomAD3 genomes AF: 0.373 AC: 56569 AN: 151810 Hom.: 12144 Cov.: 32

Gnomad AFR AF: 0.592

Gnomad AMI AF: 0.262

Gnomad AMR AF: 0.322

Gnomad ASJ AF: 0.259

Gnomad EAS AF: 0.151

Gnomad SAS AF: 0.280

Gnomad FIN AF: 0.389

Gnomad MID AF: 0.354

Gnomad NFE AF: 0.280

Gnomad OTH AF: 0.346

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

GnomAD4 genome AF: 0.373 AC: 56642 AN: 151928 Hom.: 12175 Cov.: 32 AF XY: 0.374 AC XY: 27795 AN XY: 74242

African (AFR) AF: 0.592 AC: 24538 AN: 41424

American (AMR) AF: 0.322 AC: 4918 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.259 AC: 897 AN: 3468

East Asian (EAS) AF: 0.151 AC: 783 AN: 5186

South Asian (SAS) AF: 0.280 AC: 1350 AN: 4822

European-Finnish (FIN) AF: 0.389 AC: 4096 AN: 10538

Middle Eastern (MID) AF: 0.346 AC: 101 AN: 292

European-Non Finnish (NFE) AF: 0.280 AC: 18994 AN: 67896

Other (OTH) AF: 0.345 AC: 727 AN: 2110

Alfa AF: 0.302 Hom.: 25724

Bravo AF: 0.380

Asia WGS AF: 0.292 AC: 1016 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.010
DANN	Benign	0.55
PhyloP100		-0.66
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: rs1251575; hg19: chr1-76557784;