rs1051266

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate

The NM_194255.4(SLC19A1):​c.80A>T​(p.His27Leu) variant causes a missense 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. 13/21 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: not found (cov: 32)
Exomes 𝑓: 0.0 ( 0 hom. )
Failed GnomAD Quality Control

Consequence

SLC19A1
NM_194255.4 missense

Scores

3
16

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.987
Variant links:
Genes affected
SLC19A1 (HGNC:10937): (solute carrier family 19 member 1) The membrane protein encoded by this gene is a transporter of folate and is involved in the regulation of intracellular concentrations of folate. Three transcript variants encoding different isoforms have been found for this gene.[provided by RefSeq, Mar 2011]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 0 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.0782066).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
SLC19A1NM_194255.4 linkc.80A>T p.His27Leu missense_variant Exon 2 of 6 ENST00000311124.9 NP_919231.1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
SLC19A1ENST00000311124.9 linkc.80A>T p.His27Leu missense_variant Exon 2 of 6 1 NM_194255.4 ENSP00000308895.4 P41440-1

Frequencies

GnomAD3 genomes
Cov.:
32
GnomAD4 exome
Data not reliable, filtered out with message: AC0
AF:
0.00
AC:
0
AN:
1448858
Hom.:
0
Cov.:
46
AF XY:
0.00
AC XY:
0
AN XY:
719954
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.00
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.00
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
Cov.:
32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.068
BayesDel_addAF
Uncertain
0.015
T
BayesDel_noAF
Benign
-0.22
CADD
Benign
3.7
DANN
Benign
0.39
DEOGEN2
Benign
0.13
T;T;.;T;.;T
Eigen
Benign
-1.1
Eigen_PC
Benign
-1.0
FATHMM_MKL
Benign
0.24
N
LIST_S2
Benign
0.17
T;T;T;T;T;T
M_CAP
Uncertain
0.12
D
MetaRNN
Benign
0.078
T;T;T;T;T;T
MetaSVM
Benign
-0.75
T
MutationAssessor
Benign
-1.3
.;N;N;.;.;.
PrimateAI
Benign
0.30
T
PROVEAN
Benign
0.86
N;N;N;N;N;N
REVEL
Uncertain
0.33
Sift
Benign
0.64
T;T;T;T;T;T
Sift4G
Benign
0.65
T;T;T;.;.;.
Polyphen
0.0
.;B;.;.;.;.
Vest4
0.058
MutPred
0.35
Loss of disorder (P = 0.0768);Loss of disorder (P = 0.0768);Loss of disorder (P = 0.0768);Loss of disorder (P = 0.0768);Loss of disorder (P = 0.0768);Loss of disorder (P = 0.0768);
MVP
0.67
MPC
0.12
ClinPred
0.029
T
GERP RS
2.8
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
1.0
Varity_R
0.032
gMVP
0.37

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

No publications associated with this variant yet.

Other links and lift over

hg19: chr21-46957794; API