rs1458597

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_173508.4(SLC35F3):​c.283+113358T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0811 in 152,140 control chromosomes in the GnomAD database, including 1,106 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 0.081 ( 1106 hom., cov: 32)

Consequence

SLC35F3
NM_173508.4 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.83
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 made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.96).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.211 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
SLC35F3NM_173508.4 linkuse as main transcriptc.283+113358T>C intron_variant ENST00000366618.8 NP_775779.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
SLC35F3ENST00000366618.8 linkuse as main transcriptc.283+113358T>C intron_variant 2 NM_173508.4 ENSP00000355577 Q8IY50-2

Frequencies

GnomAD3 genomes
AF:
0.0809
AC:
12294
AN:
152022
Hom.:
1098
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.214
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.0527
Gnomad ASJ
AF:
0.0305
Gnomad EAS
AF:
0.154
Gnomad SAS
AF:
0.0845
Gnomad FIN
AF:
0.0560
Gnomad MID
AF:
0.0158
Gnomad NFE
AF:
0.00849
Gnomad OTH
AF:
0.0670
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.0811
AC:
12341
AN:
152140
Hom.:
1106
Cov.:
32
AF XY:
0.0843
AC XY:
6269
AN XY:
74400
show subpopulations
Gnomad4 AFR
AF:
0.215
Gnomad4 AMR
AF:
0.0529
Gnomad4 ASJ
AF:
0.0305
Gnomad4 EAS
AF:
0.155
Gnomad4 SAS
AF:
0.0838
Gnomad4 FIN
AF:
0.0560
Gnomad4 NFE
AF:
0.00849
Gnomad4 OTH
AF:
0.0682
Alfa
AF:
0.0179
Hom.:
215
Bravo
AF:
0.0844
Asia WGS
AF:
0.124
AC:
430
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.96
CADD
Benign
0.060
DANN
Benign
0.60

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: rs1458597; hg19: chr1-234154862; API