chr2-85858688-C-T

Position:

• chr2-85858688-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_003896.4(ST3GAL5):​c.318+2493G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.554 in 151,978 control chromosomes in the GnomAD database, including 23,777 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 0.55 (23777 hom., cov: 31)
• Consequence: ST3GAL5 NM_003896.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.08

Genes affected

ST3GAL5 (HGNC:10872): (ST3 beta-galactoside alpha-2,3-sialyltransferase 5) Ganglioside GM3 is known to participate in the induction of cell differentiation, modulation of cell proliferation, maintenance of fibroblast morphology, signal transduction, and integrin-mediated cell adhesion. The protein encoded by this gene is a type II membrane protein which catalyzes the formation of GM3 using lactosylceramide as the substrate. The encoded protein is a member of glycosyltransferase family 29 and may be localized to the Golgi apparatus. Mutation in this gene has been associated with Amish infantile epilepsy syndrome. Transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.659 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ST3GAL5	NM_003896.4	c.318+2493G>A		intron_variant		ENST00000638572.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ST3GAL5	ENST00000638572.2	c.318+2493G>A		intron_variant		1	NM_003896.4	A1

Frequencies

GnomAD3 genomes AF: 0.553 AC: 84049 AN: 151860 Hom.: 23732 Cov.: 31

Gnomad AFR AF: 0.615

Gnomad AMI AF: 0.443

Gnomad AMR AF: 0.628

Gnomad ASJ AF: 0.445

Gnomad EAS AF: 0.677

Gnomad SAS AF: 0.435

Gnomad FIN AF: 0.504

Gnomad MID AF: 0.547

Gnomad NFE AF: 0.514

Gnomad OTH AF: 0.538

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

GnomAD4 genome AF: 0.554 AC: 84150 AN: 151978 Hom.: 23777 Cov.: 31 AF XY: 0.553 AC XY: 41081 AN XY: 74282

Gnomad4 AFR AF: 0.615

Gnomad4 AMR AF: 0.629

Gnomad4 ASJ AF: 0.445

Gnomad4 EAS AF: 0.678

Gnomad4 SAS AF: 0.435

Gnomad4 FIN AF: 0.504

Gnomad4 NFE AF: 0.514

Gnomad4 OTH AF: 0.541

Alfa AF: 0.471 Hom.: 2242

Bravo AF: 0.570

Asia WGS AF: 0.604 AC: 2099 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.12
DANN	Benign	0.32

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: rs4832210; hg19: chr2-86085811;