Genetic Variant ST3GAL4:p.Tyr84Tyr (chr11-126407321-C-T) – ACMG Classification: Benign (-21 pts)

Variant summary

Our verdict is Benign. The variant received -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1

The NM_001254757.2(ST3GAL4):c.252C>T(p.Tyr84Tyr) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.311 in 1,613,722 control chromosomes in the GnomAD database, including 79,495 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.32 ( 7807 hom., cov: 32)

Exomes 𝑓: 0.31 ( 71688 hom. )

Consequence

ST3GAL4
NM_001254757.2 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: -3.06

Publications

27 publications found

Variant links:

Genes affected

ST3GAL4 (HGNC:10864): (ST3 beta-galactoside alpha-2,3-sialyltransferase 4) This gene encodes a member of the glycosyltransferase 29 family, a group of enzymes involved in protein glycosylation. The encoded protein is targeted to Golgi membranes but may be proteolytically processed and secreted. The gene product may also be involved in the increased expression of sialyl Lewis X antigen seen in inflammatory responses. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Dec 2011]

ST3GAL4 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -21 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.68).

BP6

Variant 11-126407321-C-T is Benign according to our data. Variant chr11-126407321-C-T is described in ClinVar as Benign. ClinVar VariationId is 257673.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=-3.06 with no splicing effect.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.502 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ST3GAL4	NM_001254757.2 link	c.252C>T	p.Tyr84Tyr	synonymous_variant	Exon 5 of 11	ENST00000444328.7	NP_001241686.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ST3GAL4	ENST00000444328.7 link	c.252C>T	p.Tyr84Tyr	synonymous_variant	Exon 5 of 11	5	NM_001254757.2	ENSP00000394354.2		Q11206-1

Frequencies

GnomAD3 genomes

AF:

0.316

AC:

48021

AN:

151972

Hom.:

7804

Cov.:

show subpopulations

Gnomad AFR

AF:

0.344

Gnomad AMI

AF:

0.291

Gnomad AMR

AF:

0.317

Gnomad ASJ

AF:

0.362

Gnomad EAS

AF:

0.518

Gnomad SAS

AF:

0.230

Gnomad FIN

AF:

0.226

Gnomad MID

AF:

0.278

Gnomad NFE

AF:

0.301

Gnomad OTH

AF:

0.323

GnomAD2 exomes

AF:

0.316

AC:

79497

AN:

251436

AF XY:

0.310

show subpopulations

Gnomad AFR exome

AF:

0.352

Gnomad AMR exome

AF:

0.341

Gnomad ASJ exome

AF:

0.360

Gnomad EAS exome

AF:

0.514

Gnomad FIN exome

AF:

0.227

Gnomad NFE exome

AF:

0.309

Gnomad OTH exome

AF:

0.320

GnomAD4 exome

AF:

0.310

AC:

453233

AN:

1461632

Hom.:

71688

Cov.:

AF XY:

0.307

AC XY:

223550

AN XY:

727124

show subpopulations

African (AFR)

AF:

0.358

AC:

11972

AN:

33474

American (AMR)

AF:

0.332

AC:

14864

AN:

44724

Ashkenazi Jewish (ASJ)

AF:

0.361

AC:

9444

AN:

26136

East Asian (EAS)

AF:

0.474

AC:

18803

AN:

39696

South Asian (SAS)

AF:

0.232

AC:

19984

AN:

86252

European-Finnish (FIN)

AF:

0.235

AC:

12577

AN:

53410

Middle Eastern (MID)

AF:

0.264

AC:

1522

AN:

5766

European-Non Finnish (NFE)

AF:

0.310

AC:

345024

AN:

1111790

Other (OTH)

AF:

0.315

AC:

19043

AN:

60384

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.469

Heterozygous variant carriers

18656

37312

55967

74623

93279

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

11490

22980

34470

45960

57450

<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:

0.316

AC:

48054

AN:

152090

Hom.:

7807

Cov.:

AF XY:

0.312

AC XY:

23193

AN XY:

74368

show subpopulations

African (AFR)

AF:

0.343

AC:

14246

AN:

41476

American (AMR)

AF:

0.318

AC:

4855

AN:

15286

Ashkenazi Jewish (ASJ)

AF:

0.362

AC:

1257

AN:

3470

East Asian (EAS)

AF:

0.518

AC:

2683

AN:

5176

South Asian (SAS)

AF:

0.230

AC:

1112

AN:

4826

European-Finnish (FIN)

AF:

0.226

AC:

2396

AN:

10584

Middle Eastern (MID)

AF:

0.293

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.301

AC:

20480

AN:

67960

Other (OTH)

AF:

0.320

AC:

674

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

1717

3434

5152

6869

8586

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

480

960

1440

1920

2400

<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:

0.313

Hom.:

6830

Bravo

AF:

0.329

Asia WGS

AF:

0.332

AC:

1154

AN:

3478

EpiCase

AF:

0.312

EpiControl

AF:

0.306

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not specified

Benign:1

PreventionGenetics, part of Exact Sciences

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

not provided

Benign:1

Breakthrough Genomics, Breakthrough Genomics

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:not provided

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.68

CADD

Benign

0.29

(source)

DANN

Benign

0.88

PhyloP100

-3.1

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

Submissions by phenotype

Computational scores

Splicing

Publications

Other links and lift over