GeneBe

rs1225692560

Variant names:

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 2P and 2B. PM2BP4_Moderate

The NM_030965.3(ST6GALNAC5):​c.154G>A​(p.Ala52Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 15/22 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

Frequency

Genomes: not found (cov: 32)

Consequence

ST6GALNAC5
NM_030965.3 missense

Scores

1
17

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 2.30

Publications

0 publications found
Variant links:
Genes affected
ST6GALNAC5 (HGNC:19342): (ST6 N-acetylgalactosaminide alpha-2,6-sialyltransferase 5) The protein encoded by this gene is a Golgi type II transmembrane glycosyltransferase. The encoded protein catalyzes the transfer of sialic acid to cell surface proteins to modulate cell-cell interactions. Several transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Feb 2016]

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ACMG classification

Classification was made for transcript

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.117168546).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_030965.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.
GeneTranscriptTagsHGVScHGVSpEffectExon RankProteinUniProt
ST6GALNAC5
NM_030965.3
MANE Select
c.154G>Ap.Ala52Thr
missense
Exon 2 of 5NP_112227.1Q9BVH7
ST6GALNAC5
NM_001320273.2
c.154G>Ap.Ala52Thr
missense
Exon 2 of 4NP_001307202.1B4DV27
ST6GALNAC5
NM_001320274.2
c.154G>Ap.Ala52Thr
missense
Exon 2 of 3NP_001307203.1

Ensembl Transcripts

Sel.
GeneTranscriptTagsHGVScHGVSpEffectExon RankProteinUniProt
ST6GALNAC5
ENST00000477717.6
TSL:1 MANE Select
c.154G>Ap.Ala52Thr
missense
Exon 2 of 5ENSP00000417583.1Q9BVH7
ST6GALNAC5
ENST00000857213.1
c.154G>Ap.Ala52Thr
missense
Exon 2 of 4ENSP00000527272.1
ST6GALNAC5
ENST00000857212.1
c.154G>Ap.Ala52Thr
missense
Exon 2 of 4ENSP00000527271.1

Frequencies

GnomAD3 genomes
Cov.:
32
GnomAD2 exomes
AF:
0.00
AC:
0
AN:
229114
AF XY:
0.00
Gnomad AFR exome
AF:
0.00
Gnomad AMR exome
AF:
0.00
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.00
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.00
Gnomad OTH exome
AF:
0.00
GnomAD4 exome
Cov.:
31
GnomAD4 genome
Cov.:
32

ClinVar

ClinVar submissions
Significance:Uncertain significance
Revision:criteria provided, single submitter
View on ClinVar
Pathogenic
VUS
Benign
Condition
-
1
-
not specified (1)

Computational scores

Source: dbNSFP v4.9

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.068
BayesDel_addAF
Benign
-0.27
T
BayesDel_noAF
Benign
-0.62
CADD
Benign
19
DANN
Benign
0.97
DEOGEN2
Benign
0.0045
T
Eigen
Benign
-0.78
Eigen_PC
Benign
-0.68
FATHMM_MKL
Benign
0.38
N
LIST_S2
Benign
0.47
T
M_CAP
Benign
0.0086
T
MetaRNN
Benign
0.12
T
MetaSVM
Benign
-0.99
T
MutationAssessor
Benign
1.1
L
PhyloP100
2.3
PrimateAI
Uncertain
0.74
T
PROVEAN
Benign
-0.090
N
REVEL
Benign
0.067
Sift
Benign
0.14
T
Sift4G
Benign
0.74
T
Polyphen
0.049
B
Vest4
0.30
MutPred
0.30
Gain of relative solvent accessibility (P = 0.005)
MVP
0.068
MPC
0.33
ClinPred
0.15
T
GERP RS
4.0
Varity_R
0.066
gMVP
0.28
Mutation Taster
=85/15
polymorphism

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

Other links and lift over

dbSNP: rs1225692560; hg19: chr1-77334320; API