12-22296483-G-A

Variant names:

• chr12-22296483-G-A
• rs1861606
• NM_003034.4:c.237-9190C>T

Variant summary

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

The NM_003034.4(ST8SIA1):​c.237-9190C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.305 in 151,972 control chromosomes in the GnomAD database, including 7,647 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 0.31 (7647 hom., cov: 32)
• Consequence: ST8SIA1 NM_003034.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.375
• 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]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.427 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_003034.4. 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
	ST8SIA1	NM_003034.4	MANE Select	c.237-9190C>T		intron	N/A	NP_003025.1
	ST8SIA1	NM_001304450.2		c.-83-9190C>T		intron	N/A	NP_001291379.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ST8SIA1	ENST00000396037.9	TSL:1 MANE Select	c.237-9190C>T		intron	N/A	ENSP00000379353.3
	ST8SIA1	ENST00000261197.7	TSL:1	n.237-9190C>T		intron	N/A	ENSP00000261197.3
	ST8SIA1	ENST00000540824.5	TSL:4	c.90-9190C>T		intron	N/A	ENSP00000441707.1

Frequencies

GnomAD3 genomes AF: 0.305 AC: 46299 AN: 151854 Hom.: 7625 Cov.: 32

Gnomad AFR AF: 0.432

Gnomad AMI AF: 0.175

Gnomad AMR AF: 0.255

Gnomad ASJ AF: 0.288

Gnomad EAS AF: 0.338

Gnomad SAS AF: 0.393

Gnomad FIN AF: 0.193

Gnomad MID AF: 0.345

Gnomad NFE AF: 0.250

Gnomad OTH AF: 0.291

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

GnomAD4 genome AF: 0.305 AC: 46357 AN: 151972 Hom.: 7647 Cov.: 32 AF XY: 0.304 AC XY: 22617 AN XY: 74278

African (AFR) AF: 0.432 AC: 17896 AN: 41422

American (AMR) AF: 0.255 AC: 3892 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.288 AC: 1000 AN: 3470

East Asian (EAS) AF: 0.338 AC: 1741 AN: 5156

South Asian (SAS) AF: 0.392 AC: 1885 AN: 4806

European-Finnish (FIN) AF: 0.193 AC: 2042 AN: 10574

Middle Eastern (MID) AF: 0.347 AC: 102 AN: 294

European-Non Finnish (NFE) AF: 0.250 AC: 17022 AN: 67960

Other (OTH) AF: 0.292 AC: 617 AN: 2114

Alfa AF: 0.273 Hom.: 10295

Bravo AF: 0.314

Asia WGS AF: 0.334 AC: 1160 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.063
DANN	Benign	0.37
PhyloP100		-0.38
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: rs1861606; hg19: chr12-22449417;