3-187006156-A-G

Variant names:

• chr3-187006156-A-G
• rs16861460
• NM_173216.2:c.-182-32586A>G

Variant summary

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

The NM_173216.2(ST6GAL1):​c.-182-32586A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0786 in 152,236 control chromosomes in the GnomAD database, including 545 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 0.079 (545 hom., cov: 31)
  • Exomes 𝑓: 0.083 (0 hom.)
• Consequence: ST6GAL1 NM_173216.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.283
• Publications: 5 publications found

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

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.124 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_173216.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ST6GAL1	NM_173216.2	MANE Select	c.-182-32586A>G		intron	N/A	NP_775323.1
	ST6GAL1	NM_173217.2		c.-218-32586A>G		intron	N/A	NP_775324.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ST6GAL1	ENST00000169298.8	TSL:1 MANE Select	c.-182-32586A>G		intron	N/A	ENSP00000169298.3
	ST6GAL1	ENST00000485105.1	TSL:3	n.67A>G		non_coding_transcript_exon	Exon 2 of 2
	ST6GAL1	ENST00000676633.1		c.-183+9483A>G		intron	N/A	ENSP00000504448.1

Frequencies

GnomAD3 genomes AF: 0.0786 AC: 11960 AN: 152094 Hom.: 544 Cov.: 31

Gnomad AFR AF: 0.127

Gnomad AMI AF: 0.115

Gnomad AMR AF: 0.0647

Gnomad ASJ AF: 0.120

Gnomad EAS AF: 0.000192

Gnomad SAS AF: 0.0128

Gnomad FIN AF: 0.0443

Gnomad MID AF: 0.127

Gnomad NFE AF: 0.0651

Gnomad OTH AF: 0.0996

GnomAD4 exome AF: 0.0833 AC: 2 AN: 24 Hom.: 0 Cov.: 0 AF XY: 0.100 AC XY: 2 AN XY: 20

African (AFR) AC: 0 AN: 0

American (AMR) AF: 0.00 AC: 0 AN: 2

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 2

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AF: 0.00 AC: 0 AN: 2

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.125 AC: 2 AN: 16

Other (OTH) AF: 0.00 AC: 0 AN: 2

GnomAD4 genome AF: 0.0786 AC: 11963 AN: 152212 Hom.: 545 Cov.: 31 AF XY: 0.0752 AC XY: 5596 AN XY: 74410

African (AFR) AF: 0.127 AC: 5250 AN: 41500

American (AMR) AF: 0.0646 AC: 987 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.120 AC: 416 AN: 3472

East Asian (EAS) AF: 0.000193 AC: 1 AN: 5188

South Asian (SAS) AF: 0.0128 AC: 62 AN: 4830

European-Finnish (FIN) AF: 0.0443 AC: 470 AN: 10612

Middle Eastern (MID) AF: 0.139 AC: 41 AN: 294

European-Non Finnish (NFE) AF: 0.0651 AC: 4424 AN: 68008

Other (OTH) AF: 0.0981 AC: 207 AN: 2110

Alfa AF: 0.0718 Hom.: 268

Bravo AF: 0.0860

Asia WGS AF: 0.0190 AC: 67 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	5.4
DANN	Benign	0.61
PhyloP100		0.28
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: rs16861460; hg19: chr3-186723944;