rs759582

Variant names:

• chr12-22077045-A-C
• rs759582
• ENST00000544732.5:n.298-6420T>G

Your query was ambiguous. Multiple possible variants found:

• chr12-22077045-A-C
• chr12-22077045-A-T

Variant summary

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

The ENST00000544732.5(ST8SIA1):​n.298-6420T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.543 in 152,140 control chromosomes in the GnomAD database, including 23,699 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 0.54 (23699 hom., cov: 32)
• Consequence: ST8SIA1 ENST00000544732.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.319
• Publications: 3 publications found

Genes affected

ST8SIA1 (HGNC:10869): (ST8 alpha-N-acetyl-neuraminide alpha-2,8-sialyltransferase 1) Gangliosides are membrane-bound glycosphingolipids containing sialic acid. Ganglioside GD3 is known to be important for cell adhesion and growth of cultured malignant cells. The protein encoded by this gene is a type II membrane protein that catalyzes the transfer of sialic acid from CMP-sialic acid to GM3 to produce gangliosides GD3 and GT3. The encoded protein may be found in the Golgi apparatus and is a member of glycosyltransferase family 29. Alternatively spliced transcript variants have been found for this gene. [provided by RefSeq, Jan 2015]

LOC105369690 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.76).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.633 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000544732.5. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ST8SIA1	ENST00000544732.5	TSL:5	n.298-6420T>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.544 AC: 82626 AN: 152024 Hom.: 23689 Cov.: 32

Gnomad AFR AF: 0.451

Gnomad AMI AF: 0.769

Gnomad AMR AF: 0.499

Gnomad ASJ AF: 0.543

Gnomad EAS AF: 0.124

Gnomad SAS AF: 0.351

Gnomad FIN AF: 0.640

Gnomad MID AF: 0.532

Gnomad NFE AF: 0.638

Gnomad OTH AF: 0.540

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

GnomAD4 genome AF: 0.543 AC: 82670 AN: 152140 Hom.: 23699 Cov.: 32 AF XY: 0.535 AC XY: 39771 AN XY: 74364

African (AFR) AF: 0.450 AC: 18688 AN: 41488

American (AMR) AF: 0.499 AC: 7627 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.543 AC: 1884 AN: 3470

East Asian (EAS) AF: 0.124 AC: 644 AN: 5176

South Asian (SAS) AF: 0.352 AC: 1696 AN: 4820

European-Finnish (FIN) AF: 0.640 AC: 6772 AN: 10576

Middle Eastern (MID) AF: 0.517 AC: 152 AN: 294

European-Non Finnish (NFE) AF: 0.638 AC: 43372 AN: 68002

Other (OTH) AF: 0.538 AC: 1134 AN: 2108

Alfa AF: 0.460 Hom.: 1634

Bravo AF: 0.533

Asia WGS AF: 0.254 AC: 884 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
CADD	Benign	1.5
DANN	Benign	0.90
PhyloP100		0.32

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs759582; hg19: chr12-22229979;