rs201837257

Variant summary

Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_StrongBS1_SupportingBS2

The NM_080669.6(SLC46A1):​c.623A>T​(p.Tyr208Phe) variant causes a missense change. The variant allele was found at a frequency of 0.00158 in 1,613,990 control chromosomes in the GnomAD database, including 5 homozygotes. In-silico tool predicts a benign outcome for this variant. 11/17 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★★).

Frequency

Genomes: 𝑓 0.00084 ( 0 hom., cov: 32)
Exomes 𝑓: 0.0017 ( 5 hom. )

Consequence

SLC46A1
NM_080669.6 missense

Scores

3
12

Clinical Significance

Uncertain significance criteria provided, multiple submitters, no conflicts U:6

Conservation

PhyloP100: 4.70
Variant links:
Genes affected
SLC46A1 (HGNC:30521): (solute carrier family 46 member 1) This gene encodes a transmembrane proton-coupled folate transporter protein that facilitates the movement of folate and antifolate substrates across cell membranes, optimally in acidic pH environments. This protein is also expressed in the brain and choroid plexus where it transports folates into the central nervous system. This protein further functions as a heme transporter in duodenal enterocytes, and potentially in other tissues like liver and kidney. Its localization to the apical membrane or cytoplasm of intestinal cells is modulated by dietary iron levels. Mutations in this gene are associated with autosomal recessive hereditary folate malabsorption disease. Alternatively spliced transcript variants encoding different isoforms have been described for this gene. [provided by RefSeq, Aug 2013]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -9 ACMG points.

BP4
Computational evidence support a benign effect (MetaRNN=0.042482734).
BS1
Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.00084 (128/152304) while in subpopulation NFE AF= 0.00132 (90/68014). AF 95% confidence interval is 0.0011. There are 0 homozygotes in gnomad4. There are 52 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck. Existence of Clinvar submissions makes me limit the strength of this signal to Supporting
BS2
High Homozygotes in GnomAdExome4 at 5 AR gene

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
SLC46A1NM_080669.6 linkuse as main transcriptc.623A>T p.Tyr208Phe missense_variant 2/5 ENST00000612814.5 NP_542400.2

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
SLC46A1ENST00000612814.5 linkuse as main transcriptc.623A>T p.Tyr208Phe missense_variant 2/52 NM_080669.6 ENSP00000480703 P1Q96NT5-1

Frequencies

GnomAD3 genomes
AF:
0.000841
AC:
128
AN:
152186
Hom.:
0
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.000410
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.000654
Gnomad ASJ
AF:
0.000576
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.000414
Gnomad FIN
AF:
0.000377
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.00132
Gnomad OTH
AF:
0.00143
GnomAD3 exomes
AF:
0.000767
AC:
191
AN:
249100
Hom.:
0
AF XY:
0.000695
AC XY:
94
AN XY:
135180
show subpopulations
Gnomad AFR exome
AF:
0.000452
Gnomad AMR exome
AF:
0.000753
Gnomad ASJ exome
AF:
0.000498
Gnomad EAS exome
AF:
0.0000556
Gnomad SAS exome
AF:
0.000359
Gnomad FIN exome
AF:
0.000232
Gnomad NFE exome
AF:
0.00115
Gnomad OTH exome
AF:
0.000993
GnomAD4 exome
AF:
0.00165
AC:
2418
AN:
1461686
Hom.:
5
Cov.:
31
AF XY:
0.00156
AC XY:
1135
AN XY:
727128
show subpopulations
Gnomad4 AFR exome
AF:
0.000149
Gnomad4 AMR exome
AF:
0.000760
Gnomad4 ASJ exome
AF:
0.000459
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.000348
Gnomad4 FIN exome
AF:
0.000300
Gnomad4 NFE exome
AF:
0.00203
Gnomad4 OTH exome
AF:
0.00104
GnomAD4 genome
AF:
0.000840
AC:
128
AN:
152304
Hom.:
0
Cov.:
32
AF XY:
0.000698
AC XY:
52
AN XY:
74468
show subpopulations
Gnomad4 AFR
AF:
0.000409
Gnomad4 AMR
AF:
0.000654
Gnomad4 ASJ
AF:
0.000576
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.000414
Gnomad4 FIN
AF:
0.000377
Gnomad4 NFE
AF:
0.00132
Gnomad4 OTH
AF:
0.00142
Alfa
AF:
0.00131
Hom.:
0
Bravo
AF:
0.000899
TwinsUK
AF:
0.00243
AC:
9
ALSPAC
AF:
0.00182
AC:
7
ESP6500AA
AF:
0.000501
AC:
2
ESP6500EA
AF:
0.00180
AC:
15
ExAC
AF:
0.000728
AC:
88
Asia WGS
AF:
0.000289
AC:
1
AN:
3478
EpiCase
AF:
0.00136
EpiControl
AF:
0.000889

ClinVar

Significance: Uncertain significance
Submissions summary: Uncertain:6
Revision: criteria provided, multiple submitters, no conflicts
LINK: link

Submissions by phenotype

Congenital defect of folate absorption Uncertain:2
Uncertain significance, criteria provided, single submitterclinical testingFulgent Genetics, Fulgent GeneticsOct 31, 2018- -
Uncertain significance, criteria provided, single submitterclinical testingIllumina Laboratory Services, IlluminaJan 13, 2018This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score, this variant could not be ruled out of causing disease and therefore its association with disease required further investigation. A literature search was performed for the gene, cDNA change, and amino acid change (if applicable). No publications were found based on this search. This variant was therefore classified as a variant of unknown significance for this disease. -
not specified Uncertain:1
Uncertain significance, criteria provided, single submitterclinical testingGenomic Diagnostic Laboratory, Division of Genomic Diagnostics, Children's Hospital of PhiladelphiaSep 03, 2015- -
Inborn genetic diseases Uncertain:1
Uncertain significance, criteria provided, single submitterclinical testingAmbry GeneticsAug 23, 2021The c.623A>T (p.Y208F) alteration is located in exon 2 (coding exon 2) of the SLC46A1 gene. This alteration results from a A to T substitution at nucleotide position 623, causing the tyrosine (Y) at amino acid position 208 to be replaced by a phenylalanine (F). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -
not provided Uncertain:1
Uncertain significance, criteria provided, single submitterclinical testingLabcorp Genetics (formerly Invitae), LabcorpOct 13, 2022This sequence change replaces tyrosine, which is neutral and polar, with phenylalanine, which is neutral and non-polar, at codon 208 of the SLC46A1 protein (p.Tyr208Phe). This variant is present in population databases (rs201837257, gnomAD 0.1%), and has an allele count higher than expected for a pathogenic variant. This variant has not been reported in the literature in individuals affected with SLC46A1-related conditions. ClinVar contains an entry for this variant (Variation ID: 252777). Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) performed at Invitae indicates that this missense variant is not expected to disrupt SLC46A1 protein function. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. -
Intellectual disability Uncertain:1
Uncertain significance, no assertion criteria providedclinical testingCentre de Biologie Pathologie Génétique, Centre Hospitalier Universitaire de LilleJan 01, 2019- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.099
BayesDel_addAF
Benign
-0.36
T
BayesDel_noAF
Benign
-0.29
CADD
Benign
21
DANN
Benign
0.90
DEOGEN2
Benign
0.33
T;.;T;.
Eigen
Benign
-0.16
Eigen_PC
Benign
0.0096
FATHMM_MKL
Uncertain
0.89
D
LIST_S2
Uncertain
0.88
D;D;D;D
M_CAP
Benign
0.024
T
MetaRNN
Benign
0.042
T;T;T;T
MetaSVM
Benign
-1.1
T
MutationTaster
Benign
1.0
D;D
PrimateAI
Uncertain
0.56
T
Sift4G
Benign
0.20
T;T;.;.
Polyphen
0.039
B;B;.;.
Vest4
0.42
MVP
0.58
ClinPred
0.011
T
GERP RS
4.1
Varity_R
0.18
gMVP
0.55

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: rs201837257; hg19: chr17-26732092; API