GeneBe

ENST00000525071.5:c.-349+16544T>C

Variant names:

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000525071.5(SLC35F2):​c.-349+16544T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0493 in 151,754 control chromosomes in the GnomAD database, including 225 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 0.049 ( 225 hom., cov: 32)

Consequence

SLC35F2
ENST00000525071.5 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.581

Publications

1 publications found
Variant links:
Genes affected
SLC35F2 (HGNC:23615): (solute carrier family 35 member F2) Predicted to enable transmembrane transporter activity. Predicted to be involved in transmembrane transport. Predicted to be integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-1.02).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.1 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
SLC35F2ENST00000525071.5 linkc.-349+16544T>C intron_variant Intron 2 of 10 2 ENSP00000434307.1 Q8IXU6-2

Frequencies

GnomAD3 genomes
AF:
0.0493
AC:
7476
AN:
151636
Hom.:
225
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0131
Gnomad AMI
AF:
0.0901
Gnomad AMR
AF:
0.0476
Gnomad ASJ
AF:
0.0874
Gnomad EAS
AF:
0.107
Gnomad SAS
AF:
0.0586
Gnomad FIN
AF:
0.0417
Gnomad MID
AF:
0.127
Gnomad NFE
AF:
0.0651
Gnomad OTH
AF:
0.0471
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.0493
AC:
7478
AN:
151754
Hom.:
225
Cov.:
32
AF XY:
0.0488
AC XY:
3614
AN XY:
74122
show subpopulations
African (AFR)
AF:
0.0130
AC:
539
AN:
41404
American (AMR)
AF:
0.0475
AC:
722
AN:
15212
Ashkenazi Jewish (ASJ)
AF:
0.0874
AC:
303
AN:
3466
East Asian (EAS)
AF:
0.107
AC:
554
AN:
5158
South Asian (SAS)
AF:
0.0586
AC:
281
AN:
4794
European-Finnish (FIN)
AF:
0.0417
AC:
439
AN:
10528
Middle Eastern (MID)
AF:
0.129
AC:
38
AN:
294
European-Non Finnish (NFE)
AF:
0.0651
AC:
4420
AN:
67886
Other (OTH)
AF:
0.0476
AC:
100
AN:
2102
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.498
Heterozygous variant carriers
0
354
708
1062
1416
1770
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
94
188
282
376
470
<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:
0.0586
Hom.:
152
Bravo
AF:
0.0475
Asia WGS
AF:
0.0850
AC:
296
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-1.0
CADD
Benign
0.93
DANN
Benign
0.11
PhyloP100
-0.58
Mutation Taster
=100/0
polymorphism (auto)

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

Other links and lift over

dbSNP: rs12800508; hg19: chr11-107762623; API