Genetic Variant NM_015879.3: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:

Genome browser will be placed here

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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ST8SIA3	NM_015879.3 link	c.*18C>T		3_prime_UTR_variant	Exon 4 of 4	ENST00000324000.4	NP_056963.2	O43173Q59GW3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ST8SIA3	ENST00000324000.4 link	c.*18C>T		3_prime_UTR_variant	Exon 4 of 4	1	NM_015879.3	ENSP00000320431.2		O43173

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 v4.3

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

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over