Genetic Variant ST8SIA3:c.*18C>T (chr18-57360295-C-T) – ACMG Classification: Benign (-10 pts)

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_ModerateBA1

The NM_015879.3(ST8SIA3):c.*18C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.198 in 1,602,964 control chromosomes in the GnomAD database, including 37,294 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 0.26 ( 6146 hom., cov: 33)

Exomes 𝑓: 0.19 ( 31148 hom. )

Consequence

ST8SIA3
NM_015879.3 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 2.91

Publications

12 publications found

Variant links:

Genes affected

ST8SIA3 (HGNC:14269): (ST8 alpha-N-acetyl-neuraminide alpha-2,8-sialyltransferase 3) Enables alpha-N-acetylneuraminate alpha-2,8-sialyltransferase activity and identical protein binding activity. Involved in several processes, including ganglioside biosynthetic process; glycoprotein metabolic process; and protein sialylation. Predicted to be located in Golgi membrane. [provided by Alliance of Genome Resources, Apr 2022]

ST8SIA3 links:

ENSG00000293721 (HGNC:):

ENSG00000293721 links:

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -10 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.45).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.495 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_015879.3. 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
	ST8SIA3	NM_015879.3	MANE Select	c.*18C>T		3_prime_UTR	Exon 4 of 4	NP_056963.2	O43173

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
ST8SIA3	ENST00000324000.4	TSL:1 MANE Select	c.*18C>T	3_prime_UTR	Exon 4 of 4	ENSP00000320431.2	O43173
ST8SIA3	ENST00000586360.1	TSL:3	c.317+2825C>T	intron	N/A	ENSP00000467752.1	K7EQB3
ENSG00000293721	ENST00000718553.1		n.60+63581G>A	intron	N/A

Frequencies

GnomAD3 genomes

AF:

0.260

AC:

39490

AN:

151968

Hom.:

6130

Cov.:

show subpopulations

Gnomad AFR

AF:

0.395

Gnomad AMI

AF:

0.308

Gnomad AMR

AF:

0.281

Gnomad ASJ

AF:

0.123

Gnomad EAS

AF:

0.511

Gnomad SAS

AF:

0.291

Gnomad FIN

AF:

0.225

Gnomad MID

AF:

0.130

Gnomad NFE

AF:

0.165

Gnomad OTH

AF:

0.221

GnomAD2 exomes

AF:

0.245

AC:

60306

AN:

245758

AF XY:

0.237

show subpopulations

Gnomad AFR exome

AF:

0.391

Gnomad AMR exome

AF:

0.313

Gnomad ASJ exome

AF:

0.127

Gnomad EAS exome

AF:

0.509

Gnomad FIN exome

AF:

0.226

Gnomad NFE exome

AF:

0.167

Gnomad OTH exome

AF:

0.204

GnomAD4 exome

AF:

0.192

AC:

278014

AN:

1450878

Hom.:

31148

Cov.:

AF XY:

0.193

AC XY:

138704

AN XY:

720208

show subpopulations

African (AFR)

AF:

0.397

AC:

13140

AN:

33084

American (AMR)

AF:

0.309

AC:

13571

AN:

43906

Ashkenazi Jewish (ASJ)

AF:

0.129

AC:

3322

AN:

25822

East Asian (EAS)

AF:

0.519

AC:

20470

AN:

39448

South Asian (SAS)

AF:

0.280

AC:

23911

AN:

85440

European-Finnish (FIN)

AF:

0.225

AC:

11936

AN:

53060

Middle Eastern (MID)

AF:

0.138

AC:

777

AN:

5648

European-Non Finnish (NFE)

AF:

0.162

AC:

178703

AN:

1104604

Other (OTH)

AF:

0.204

AC:

12184

AN:

59866

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.468

Heterozygous variant carriers

9758

19515

29273

39030

48788

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

6748

13496

20244

26992

33740

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.260

AC:

39563

AN:

152086

Hom.:

6146

Cov.:

AF XY:

0.266

AC XY:

19746

AN XY:

74344

show subpopulations

African (AFR)

AF:

0.395

AC:

16398

AN:

41486

American (AMR)

AF:

0.281

AC:

4297

AN:

15272

Ashkenazi Jewish (ASJ)

AF:

0.123

AC:

427

AN:

3470

East Asian (EAS)

AF:

0.511

AC:

2639

AN:

5164

South Asian (SAS)

AF:

0.290

AC:

1397

AN:

4818

European-Finnish (FIN)

AF:

0.225

AC:

2372

AN:

10564

Middle Eastern (MID)

AF:

0.146

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.165

AC:

11235

AN:

67994

Other (OTH)

AF:

0.225

AC:

475

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

1424

2848

4273

5697

7121

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

386

772

1158

1544

1930

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.192

Hom.:

4571

Bravo

AF:

0.269

Asia WGS

AF:

0.399

AC:

1385

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.45

CADD

Benign

(source)

DANN

Benign

0.91

PhyloP100

2.9

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over