chr3-187014937-G-A

Position:

• chr3-187014937-G-A

Variant summary

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

The NM_173216.2(ST6GAL1):​c.-182-23805G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.34 in 151,964 control chromosomes in the GnomAD database, including 9,259 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 0.34 (9259 hom., cov: 32)
• Consequence: ST6GAL1 NM_173216.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.222

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 (EAS) allele frequency at 95% confidence interval = 0.397 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ST6GAL1	NM_173216.2	c.-182-23805G>A		intron_variant		ENST00000169298.8	NP_775323.1
ST6GAL1	NM_173217.2	c.-218-23805G>A		intron_variant			NP_775324.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ST6GAL1	ENST00000169298.8	c.-182-23805G>A		intron_variant		1	NM_173216.2	ENSP00000169298.3

Frequencies

GnomAD3 genomes AF: 0.340 AC: 51678 AN: 151846 Hom.: 9252 Cov.: 32

Gnomad AFR AF: 0.231

Gnomad AMI AF: 0.117

Gnomad AMR AF: 0.398

Gnomad ASJ AF: 0.411

Gnomad EAS AF: 0.410

Gnomad SAS AF: 0.404

Gnomad FIN AF: 0.383

Gnomad MID AF: 0.269

Gnomad NFE AF: 0.378

Gnomad OTH AF: 0.324

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

GnomAD4 genome AF: 0.340 AC: 51713 AN: 151964 Hom.: 9259 Cov.: 32 AF XY: 0.342 AC XY: 25354 AN XY: 74242

Gnomad4 AFR AF: 0.231

Gnomad4 AMR AF: 0.399

Gnomad4 ASJ AF: 0.411

Gnomad4 EAS AF: 0.411

Gnomad4 SAS AF: 0.403

Gnomad4 FIN AF: 0.383

Gnomad4 NFE AF: 0.378

Gnomad4 OTH AF: 0.324

Alfa AF: 0.371 Hom.: 5074

Bravo AF: 0.337

Asia WGS AF: 0.404 AC: 1403 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	1.4
DANN	Benign	0.54

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: rs3821819; hg19: chr3-186732725;