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GeneBe

12-104844552-T-C

Variant summary

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

The NM_001352171.3(SLC41A2):c.1456A>G(p.Thr486Ala) variant causes a missense change. The variant allele was found at a frequency of 0.000000703 in 1,422,520 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

Frequency

Genomes: not found (cov: 32)
Exomes 𝑓: 7.0e-7 ( 0 hom. )

Consequence

SLC41A2
NM_001352171.3 missense

Scores

7
12

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 5.62
Variant links:
Genes affected
SLC41A2 (HGNC:31045): (solute carrier family 41 member 2) Predicted to enable inorganic cation transmembrane transporter activity. Predicted to be involved in magnesium ion transmembrane transport. Predicted to act upstream of or within metal ion transport. Predicted to be integral component of membrane. Predicted to be active in plasma membrane. [provided by Alliance of Genome Resources, Apr 2022]

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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=0.19441095).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
SLC41A2NM_001352171.3 linkuse as main transcriptc.1456A>G p.Thr486Ala missense_variant 10/11 ENST00000258538.8

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
SLC41A2ENST00000258538.8 linkuse as main transcriptc.1456A>G p.Thr486Ala missense_variant 10/111 NM_001352171.3 P1

Frequencies

GnomAD3 genomes
Cov.:
32
GnomAD4 exome
AF:
7.03e-7
AC:
1
AN:
1422520
Hom.:
0
Cov.:
26
AF XY:
0.00
AC XY:
0
AN XY:
706860
show subpopulations
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:
0.0000170
GnomAD4 genome
Cov.:
32
Bravo
AF:
0.0000113

ClinVar

Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not specified Uncertain:1
Uncertain significance, criteria provided, single submitterclinical testingAmbry GeneticsDec 21, 2022The c.1456A>G (p.T486A) alteration is located in exon 9 (coding exon 9) of the SLC41A2 gene. This alteration results from a A to G substitution at nucleotide position 1456, causing the threonine (T) at amino acid position 486 to be replaced by an alanine (A). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.10
BayesDel_addAF
Uncertain
0.16
D
BayesDel_noAF
Uncertain
-0.010
Cadd
Benign
22
Dann
Uncertain
0.99
DEOGEN2
Benign
0.23
T
Eigen
Benign
-0.068
Eigen_PC
Benign
0.14
FATHMM_MKL
Uncertain
0.96
D
LIST_S2
Uncertain
0.88
D
M_CAP
Benign
0.0062
T
MetaRNN
Benign
0.19
T
MetaSVM
Benign
-1.1
T
MutationAssessor
Benign
1.4
L
MutationTaster
Benign
1.0
D
PrimateAI
Uncertain
0.62
T
PROVEAN
Uncertain
-3.0
D
REVEL
Benign
0.20
Sift
Benign
0.19
T
Sift4G
Benign
0.23
T
Polyphen
0.051
B
Vest4
0.30
MutPred
0.47
Gain of catalytic residue at T486 (P = 0);
MVP
0.082
MPC
0.56
ClinPred
0.92
D
GERP RS
5.6
Varity_R
0.34
gMVP
0.65

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: rs1170376633; hg19: chr12-105238330; API