chr3-187005156-G-A

Position:

• chr3-187005156-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.-182-33586G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.862 in 152,054 control chromosomes in the GnomAD database, including 56,579 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 0.86 (56579 hom., cov: 31)
• Consequence: ST6GAL1 NM_173216.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.180

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=-1.08).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.875 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ST6GAL1	NM_173216.2	c.-182-33586G>A		intron_variant		ENST00000169298.8	NP_775323.1
ST6GAL1	NM_173217.2	c.-218-33586G>A		intron_variant			NP_775324.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ST6GAL1	ENST00000169298.8	c.-182-33586G>A		intron_variant		1	NM_173216.2	ENSP00000169298	P1

Frequencies

GnomAD3 genomes AF: 0.862 AC: 130995 AN: 151936 Hom.: 56534 Cov.: 31

Gnomad AFR AF: 0.883

Gnomad AMI AF: 0.868

Gnomad AMR AF: 0.885

Gnomad ASJ AF: 0.932

Gnomad EAS AF: 0.896

Gnomad SAS AF: 0.864

Gnomad FIN AF: 0.856

Gnomad MID AF: 0.861

Gnomad NFE AF: 0.839

Gnomad OTH AF: 0.860

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

GnomAD4 genome AF: 0.862 AC: 131101 AN: 152054 Hom.: 56579 Cov.: 31 AF XY: 0.863 AC XY: 64205 AN XY: 74366

Gnomad4 AFR AF: 0.883

Gnomad4 AMR AF: 0.885

Gnomad4 ASJ AF: 0.932

Gnomad4 EAS AF: 0.895

Gnomad4 SAS AF: 0.863

Gnomad4 FIN AF: 0.856

Gnomad4 NFE AF: 0.839

Gnomad4 OTH AF: 0.861

Alfa AF: 0.850 Hom.: 53326

Bravo AF: 0.866

Asia WGS AF: 0.911 AC: 3169 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.76
DANN	Benign	0.47

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: rs7652995; hg19: chr3-186722944;