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GeneBe

11-126408180-C-T

Variant summary

Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BA1

The NM_001254757.2(ST3GAL4):c.423C>T(p.Tyr141=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.309 in 1,613,724 control chromosomes in the GnomAD database, including 78,523 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.32 ( 7782 hom., cov: 32)
Exomes 𝑓: 0.31 ( 70741 hom. )

Consequence

ST3GAL4
NM_001254757.2 synonymous

Scores

2

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.932
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]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -15 ACMG points.

BP4
?
    BP4 - Multiple lines of computational evidence suggest no impact on gene or gene product (conservation, evolutionary, splicing impact, etc.)
Computational evidence support a benign effect (BayesDel_noAF=-0.5).
BP6
?
    BP6 - Reputable source recently reports variant as benign, but the evidence is not available to the laboratory to perform an independent evaluation
Variant 11-126408180-C-T is Benign according to our data. Variant chr11-126408180-C-T is described in ClinVar as [Benign]. Clinvar id is 257674.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
    BP7 - A synonymous (silent) variant for which splicing prediction algorithms predict no impact to the splice consensus sequence nor the creation of a new splice site AND the nucleotide is not highly conserved
Synonymous conserved (PhyloP=-0.932 with no splicing effect.
BA1
?
    BA1 - Allele frequency is >5% in Exome Sequencing Project, 1000 Genomes Project, or Exome Aggregation Consortium
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.499 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
ST3GAL4NM_001254757.2 linkuse as main transcriptc.423C>T p.Tyr141= synonymous_variant 7/11 ENST00000444328.7

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
ST3GAL4ENST00000444328.7 linkuse as main transcriptc.423C>T p.Tyr141= synonymous_variant 7/115 NM_001254757.2 P4Q11206-1

Frequencies

GnomAD3 genomes
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.315
AC:
47892
AN:
151904
Hom.:
7779
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.345
Gnomad AMI
AF:
0.290
Gnomad AMR
AF:
0.322
Gnomad ASJ
AF:
0.364
Gnomad EAS
AF:
0.515
Gnomad SAS
AF:
0.231
Gnomad FIN
AF:
0.221
Gnomad MID
AF:
0.278
Gnomad NFE
AF:
0.299
Gnomad OTH
AF:
0.324
GnomAD3 exomes
AF:
0.314
AC:
78937
AN:
251328
Hom.:
13122
AF XY:
0.308
AC XY:
41825
AN XY:
135838
show subpopulations
Gnomad AFR exome
AF:
0.353
Gnomad AMR exome
AF:
0.340
Gnomad ASJ exome
AF:
0.362
Gnomad EAS exome
AF:
0.512
Gnomad SAS exome
AF:
0.226
Gnomad FIN exome
AF:
0.220
Gnomad NFE exome
AF:
0.306
Gnomad OTH exome
AF:
0.317
GnomAD4 exome
AF:
0.308
AC:
450462
AN:
1461702
Hom.:
70741
Cov.:
45
AF XY:
0.305
AC XY:
222088
AN XY:
727138
show subpopulations
Gnomad4 AFR exome
AF:
0.358
Gnomad4 AMR exome
AF:
0.332
Gnomad4 ASJ exome
AF:
0.363
Gnomad4 EAS exome
AF:
0.469
Gnomad4 SAS exome
AF:
0.233
Gnomad4 FIN exome
AF:
0.229
Gnomad4 NFE exome
AF:
0.308
Gnomad4 OTH exome
AF:
0.314
GnomAD4 genome
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.315
AC:
47924
AN:
152022
Hom.:
7782
Cov.:
32
AF XY:
0.311
AC XY:
23139
AN XY:
74284
show subpopulations
Gnomad4 AFR
AF:
0.345
Gnomad4 AMR
AF:
0.322
Gnomad4 ASJ
AF:
0.364
Gnomad4 EAS
AF:
0.515
Gnomad4 SAS
AF:
0.231
Gnomad4 FIN
AF:
0.221
Gnomad4 NFE
AF:
0.299
Gnomad4 OTH
AF:
0.321
Alfa
AF:
0.309
Hom.:
17287
Bravo
AF:
0.329
Asia WGS
AF:
0.328
AC:
1140
AN:
3478
EpiCase
AF:
0.309
EpiControl
AF:
0.304

ClinVar

Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not specified Benign:1
Benign, criteria provided, single submitterclinical testingPreventionGenetics, part of Exact Sciences-- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.50
Cadd
Benign
3.1
Dann
Benign
0.72

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

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs2230279; hg19: chr11-126278075; COSMIC: COSV57106561; COSMIC: COSV57106561; API