rs189132172

Variant names:

• chr2-85889181-C-G
• rs189132172
• ENST00000640418.1:c.139+4627G>C

Your query was ambiguous. Multiple possible variants found:

• chr2-85889181-C-G
• chr2-85889181-C-T

Variant summary

Our verdict is Benign. The variant received -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The ENST00000638258.1(ST3GAL5):​c.-3+4627G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.018 in 275,132 control chromosomes in the GnomAD database, including 238 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.029 (223 hom., cov: 32)
  • Exomes 𝑓: 0.0038 (15 hom.)
• Consequence: ST3GAL5 ENST00000638258.1 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.615
• Publications: 0 publications found

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]

ST3GAL5-AS1 (HGNC:51129): (ST3GAL5 antisense RNA 1 (head to head))

ACMG classification

Our verdict: Benign. The variant received -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BP6: Variant 2-85889181-C-G is Benign according to our data. Variant chr2-85889181-C-G is described in ClinVar as Benign. ClinVar VariationId is 1284093.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.1 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000638258.1. 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
	ST3GAL5	NM_003896.4	MANE Select	c.-276G>C		upstream_gene	N/A	NP_003887.3
	ST3GAL5	NM_001354227.2		c.-547G>C		upstream_gene	N/A	NP_001341156.1	A0A0S2Z4S6
	ST3GAL5	NM_001354229.2		c.-491G>C		upstream_gene	N/A	NP_001341158.1	A0A0S2Z4S6

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ST3GAL5	ENST00000640418.1	TSL:5	c.139+4627G>C		intron	N/A	ENSP00000492098.1	A0A1W2PQR0
	ST3GAL5	ENST00000640322.1	TSL:5	c.-3+4627G>C		intron	N/A	ENSP00000491564.1	Q9UNP4-2
	ST3GAL5	ENST00000638258.1	TSL:3	c.-3+4627G>C		intron	N/A	ENSP00000491126.1	A0A1W2PPF6

Frequencies

GnomAD3 genomes AF: 0.0294 AC: 4474 AN: 152114 Hom.: 224 Cov.: 32

Gnomad AFR AF: 0.103

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00890

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.000828

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.0191

Gnomad NFE AF: 0.000309

Gnomad OTH AF: 0.0201

GnomAD4 exome AF: 0.00380 AC: 467 AN: 122902 Hom.: 15 Cov.: 0 AF XY: 0.00294 AC XY: 186 AN XY: 63206

African (AFR) AF: 0.0973 AC: 326 AN: 3352

American (AMR) AF: 0.00802 AC: 28 AN: 3490

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 4408

East Asian (EAS) AF: 0.00 AC: 0 AN: 10462

South Asian (SAS) AF: 0.00 AC: 0 AN: 1148

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 11432

Middle Eastern (MID) AF: 0.00297 AC: 2 AN: 674

European-Non Finnish (NFE) AF: 0.000413 AC: 33 AN: 79824

Other (OTH) AF: 0.00962 AC: 78 AN: 8112

GnomAD4 genome AF: 0.0294 AC: 4477 AN: 152230 Hom.: 223 Cov.: 32 AF XY: 0.0287 AC XY: 2140 AN XY: 74436

African (AFR) AF: 0.103 AC: 4270 AN: 41540

American (AMR) AF: 0.00889 AC: 136 AN: 15306

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3466

East Asian (EAS) AF: 0.00 AC: 0 AN: 5170

South Asian (SAS) AF: 0.000621 AC: 3 AN: 4828

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 10616

Middle Eastern (MID) AF: 0.0171 AC: 5 AN: 292

European-Non Finnish (NFE) AF: 0.000309 AC: 21 AN: 67988

Other (OTH) AF: 0.0199 AC: 42 AN: 2114

Alfa AF: 0.000274 Hom.: 0

Bravo AF: 0.0332

ClinVar

ClinVar submissions

Significance: Benign

Revision: criteria provided, single submitter

Pathogenic	VUS	Benign	Condition
-	-	1	not provided (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	2.0
DANN	Benign	0.50
PhyloP100		-0.61
PromoterAI		-0.0038	Neutral

Splicing

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

Other links and lift over

dbSNP: rs189132172; hg19: chr2-86116304;