rs2239612

Variant names:

• chr3-187075454-G-A
• rs2239612
• NM_173216.2:c.980-108G>A

Your query was ambiguous. Multiple possible variants found:

• chr3-187075454-G-A
• chr3-187075454-G-C
• chr3-187075454-G-T

Variant summary

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

The NM_173216.2(ST6GAL1):​c.980-108G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.13 in 1,500,714 control chromosomes in the GnomAD database, including 14,309 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 0.17 (2658 hom., cov: 32)
  • Exomes 𝑓: 0.13 (11651 hom.)
• Consequence: ST6GAL1 NM_173216.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.09
• Publications: 20 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=-0.84).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.272 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ST6GAL1	NM_173216.2	MANE Select	c.980-108G>A		intron	N/A	NP_775323.1	P15907-1
	ST6GAL1	NM_001353916.2		c.980-108G>A		intron	N/A	NP_001340845.1	P15907-1
	ST6GAL1	NM_003032.3		c.980-108G>A		intron	N/A	NP_003023.1	P15907-1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ST6GAL1	ENST00000169298.8	TSL:1 MANE Select	c.980-108G>A		intron	N/A	ENSP00000169298.3	P15907-1
	ST6GAL1	ENST00000448044.5	TSL:1	c.980-108G>A		intron	N/A	ENSP00000389337.1	P15907-1
	ST6GAL1	ENST00000912781.1		c.1001-108G>A		intron	N/A	ENSP00000582840.1

Frequencies

GnomAD3 genomes AF: 0.172 AC: 26108 AN: 151992 Hom.: 2642 Cov.: 32

Gnomad AFR AF: 0.276

Gnomad AMI AF: 0.0822

Gnomad AMR AF: 0.206

Gnomad ASJ AF: 0.0985

Gnomad EAS AF: 0.177

Gnomad SAS AF: 0.110

Gnomad FIN AF: 0.136

Gnomad MID AF: 0.187

Gnomad NFE AF: 0.115

Gnomad OTH AF: 0.174

GnomAD4 exome AF: 0.125 AC: 168776 AN: 1348604 Hom.: 11651 AF XY: 0.124 AC XY: 82093 AN XY: 664670

African (AFR) AF: 0.289 AC: 8847 AN: 30574

American (AMR) AF: 0.263 AC: 9380 AN: 35662

Ashkenazi Jewish (ASJ) AF: 0.0972 AC: 2062 AN: 21222

East Asian (EAS) AF: 0.186 AC: 7232 AN: 38794

South Asian (SAS) AF: 0.102 AC: 7396 AN: 72382

European-Finnish (FIN) AF: 0.139 AC: 6355 AN: 45594

Middle Eastern (MID) AF: 0.180 AC: 700 AN: 3896

European-Non Finnish (NFE) AF: 0.114 AC: 119253 AN: 1044630

Other (OTH) AF: 0.135 AC: 7551 AN: 55850

GnomAD4 genome AF: 0.172 AC: 26157 AN: 152110 Hom.: 2658 Cov.: 32 AF XY: 0.172 AC XY: 12813 AN XY: 74372

African (AFR) AF: 0.277 AC: 11477 AN: 41484

American (AMR) AF: 0.206 AC: 3151 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.0985 AC: 342 AN: 3472

East Asian (EAS) AF: 0.176 AC: 911 AN: 5164

South Asian (SAS) AF: 0.110 AC: 528 AN: 4820

European-Finnish (FIN) AF: 0.136 AC: 1440 AN: 10592

Middle Eastern (MID) AF: 0.180 AC: 53 AN: 294

European-Non Finnish (NFE) AF: 0.115 AC: 7809 AN: 67998

Other (OTH) AF: 0.176 AC: 371 AN: 2110

Alfa AF: 0.137 Hom.: 4027

Bravo AF: 0.187

Asia WGS AF: 0.171 AC: 594 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	0.41
DANN	Benign	0.50
PhyloP100		-1.1
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: rs2239612; hg19: chr3-186793242; COSMIC: COSV51471595; COSMIC: COSV51471595;