rs10513807

Positions:

• chr3-186938324-G-A
• chr3-186938324-G-C
• chr3-186938324-G-T

Variant summary

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

The ENST00000169298.8(ST6GAL1):​c.-325+7490G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.508 in 152,026 control chromosomes in the GnomAD database, including 19,725 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 0.51 (19725 hom., cov: 32)
• Consequence: ST6GAL1 ENST00000169298.8 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.364

Genes affected

ST6GAL1 (HGNC:10860): (ST6 beta-galactoside alpha-2,6-sialyltransferase 1) This gene encodes a member of glycosyltransferase family 29. The encoded protein is a type II membrane protein that catalyzes the transfer of sialic acid from CMP-sialic acid to galactose-containing substrates. The protein, which is normally found in the Golgi but can be proteolytically processed to a soluble form, is involved in the generation of the cell-surface carbohydrate determinants and differentiation antigens HB-6, CD75, and CD76. This gene has been incorrectly referred to as CD75. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jul 2017]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.565 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ST6GAL1	NM_173216.2	c.-325+7490G>A		intron_variant		ENST00000169298.8	NP_775323.1
ST6GAL1	NM_173217.2	c.-361+7490G>A		intron_variant			NP_775324.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ST6GAL1	ENST00000169298.8	c.-325+7490G>A		intron_variant		1	NM_173216.2	ENSP00000169298	P1

Frequencies

GnomAD3 genomes AF: 0.508 AC: 77181 AN: 151908 Hom.: 19714 Cov.: 32

Gnomad AFR AF: 0.432

Gnomad AMI AF: 0.631

Gnomad AMR AF: 0.575

Gnomad ASJ AF: 0.555

Gnomad EAS AF: 0.557

Gnomad SAS AF: 0.580

Gnomad FIN AF: 0.555

Gnomad MID AF: 0.491

Gnomad NFE AF: 0.519

Gnomad OTH AF: 0.527

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

GnomAD4 genome AF: 0.508 AC: 77245 AN: 152026 Hom.: 19725 Cov.: 32 AF XY: 0.513 AC XY: 38149 AN XY: 74302

Gnomad4 AFR AF: 0.432

Gnomad4 AMR AF: 0.575

Gnomad4 ASJ AF: 0.555

Gnomad4 EAS AF: 0.558

Gnomad4 SAS AF: 0.581

Gnomad4 FIN AF: 0.555

Gnomad4 NFE AF: 0.519

Gnomad4 OTH AF: 0.527

Alfa AF: 0.515 Hom.: 26614

Bravo AF: 0.505

Asia WGS AF: 0.568 AC: 1977 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.55
DANN	Benign	0.51

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: rs10513807; hg19: chr3-186656113;