GeneBe

NM_173508.4:c.284-63194G>T

Variant names:

Variant summary

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

The NM_173508.4(SLC35F3):​c.284-63194G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.648 in 152,212 control chromosomes in the GnomAD database, including 39,479 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 0.65 ( 39479 hom., cov: 33)

Consequence

SLC35F3
NM_173508.4 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.919

Publications

0 publications found
Variant links:
Genes affected
SLC35F3 (HGNC:23616): (solute carrier family 35 member F3) Involved in thiamine 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=-0.81).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.903 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
SLC35F3NM_173508.4 linkc.284-63194G>T intron_variant Intron 2 of 7 ENST00000366618.8 NP_775779.1 Q8IY50-2

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
SLC35F3ENST00000366618.8 linkc.284-63194G>T intron_variant Intron 2 of 7 2 NM_173508.4 ENSP00000355577.3 Q8IY50-2

Frequencies

GnomAD3 genomes
AF:
0.648
AC:
98633
AN:
152094
Hom.:
39478
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.216
Gnomad AMI
AF:
0.939
Gnomad AMR
AF:
0.601
Gnomad ASJ
AF:
0.886
Gnomad EAS
AF:
0.142
Gnomad SAS
AF:
0.649
Gnomad FIN
AF:
0.868
Gnomad MID
AF:
0.807
Gnomad NFE
AF:
0.909
Gnomad OTH
AF:
0.682
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.648
AC:
98633
AN:
152212
Hom.:
39479
Cov.:
33
AF XY:
0.641
AC XY:
47702
AN XY:
74412
show subpopulations
African (AFR)
AF:
0.215
AC:
8936
AN:
41524
American (AMR)
AF:
0.601
AC:
9186
AN:
15292
Ashkenazi Jewish (ASJ)
AF:
0.886
AC:
3073
AN:
3468
East Asian (EAS)
AF:
0.142
AC:
733
AN:
5168
South Asian (SAS)
AF:
0.652
AC:
3140
AN:
4816
European-Finnish (FIN)
AF:
0.868
AC:
9208
AN:
10606
Middle Eastern (MID)
AF:
0.803
AC:
236
AN:
294
European-Non Finnish (NFE)
AF:
0.909
AC:
61840
AN:
68020
Other (OTH)
AF:
0.675
AC:
1425
AN:
2112
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.504
Heterozygous variant carriers
0
1037
2074
3110
4147
5184
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
730
1460
2190
2920
3650
<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:
0.772
Hom.:
6174
Bravo
AF:
0.605
Asia WGS
AF:
0.401
AC:
1396
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.81
CADD
Benign
5.6
DANN
Benign
0.83
PhyloP100
0.92
Mutation Taster
=100/0
polymorphism (auto)

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: rs2045520; hg19: chr1-234303969; API