GeneBe

6-25914573-G-T

Variant names:

Variant summary

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

The NM_001286123.3(SLC17A2):​c.1302+7C>A variant causes a splice region, intron 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. 1/1 splice prediction tools predict no significant impact on normal splicing. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: not found (cov: 31)
Exomes 𝑓: 0.0 ( 0 hom. )
Failed GnomAD Quality Control

Consequence

SLC17A2
NM_001286123.3 splice_region, intron

Scores

1
15

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.10

Publications

26 publications found
Variant links:
Genes affected
SLC17A2 (HGNC:10930): (solute carrier family 17 member 2) Predicted to enable sialic acid transmembrane transporter activity. Predicted to be involved in sialic acid transport. Predicted to be located in membrane. Predicted to be active in lysosome. Predicted to be integral component of plasma membrane. [provided by Alliance of Genome Resources, Apr 2022]

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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=0.182464).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001286123.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.
GeneTranscriptTagsHGVScHGVSpEffectExon RankProteinUniProt
SLC17A2
NM_001286123.3
MANE Select
c.1302+7C>A
splice_region intron
N/ANP_001273052.1O00624-3
SLC17A2
NM_001286125.2
c.1161C>Ap.Gly387Gly
synonymous
Exon 9 of 10NP_001273054.1
SLC17A2
NM_005835.4
c.1154+7C>A
splice_region intron
N/ANP_005826.1O00624-2

Ensembl Transcripts

Sel.
GeneTranscriptTagsHGVScHGVSpEffectExon RankProteinUniProt
SLC17A2
ENST00000377850.8
TSL:5 MANE Select
c.1302+7C>A
splice_region intron
N/AENSP00000367081.3O00624-3
SLC17A2
ENST00000360488.7
TSL:1
c.1154+7C>A
splice_region intron
N/AENSP00000353677.3O00624-2
SLC17A2
ENST00000265425.3
TSL:5
c.1309C>Ap.Pro437Thr
missense
Exon 10 of 11ENSP00000265425.3O00624-1

Frequencies

GnomAD3 genomes
Cov.:
31
GnomAD4 exome
Data not reliable, filtered out with message: AC0
AF:
0.00
AC:
0
AN:
1436046
Hom.:
0
Cov.:
27
AF XY:
0.00
AC XY:
0
AN XY:
716064
African (AFR)
AF:
0.00
AC:
0
AN:
33156
American (AMR)
AF:
0.00
AC:
0
AN:
44628
Ashkenazi Jewish (ASJ)
AF:
0.00
AC:
0
AN:
25986
East Asian (EAS)
AF:
0.00
AC:
0
AN:
39510
South Asian (SAS)
AF:
0.00
AC:
0
AN:
85690
European-Finnish (FIN)
AF:
0.00
AC:
0
AN:
53384
Middle Eastern (MID)
AF:
0.00
AC:
0
AN:
5706
European-Non Finnish (NFE)
AF:
0.00
AC:
0
AN:
1088392
Other (OTH)
AF:
0.00
AC:
0
AN:
59594
GnomAD4 genome
Cov.:
31

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.064
BayesDel_addAF
Benign
-0.22
T
BayesDel_noAF
Benign
-0.55
CADD
Benign
13
DANN
Benign
0.78
DEOGEN2
Benign
0.051
T
Eigen
Benign
0.17
Eigen_PC
Benign
-0.12
FATHMM_MKL
Benign
0.072
N
LIST_S2
Benign
0.28
T
M_CAP
Benign
0.0029
T
MetaRNN
Benign
0.18
T
MetaSVM
Benign
-1.0
T
PhyloP100
1.1
PROVEAN
Benign
-1.3
N
REVEL
Benign
0.070
Sift
Benign
0.36
T
Sift4G
Pathogenic
0.0
D
Vest4
0.10
MutPred
0.28
Gain of glycosylation at P437 (P = 0.0462)
MVP
0.53
ClinPred
0.086
T
GERP RS
1.7
Varity_R
0.064
Mutation Taster
=97/3
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: rs2071299; hg19: chr6-25914801; API