1-205791697-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 3 ACMG points: 3P and 0B. PM2PP3
The NM_173854.6(SLC41A1):c.1378G>A(p.Ala460Thr) variant causes a missense change. The variant allele was found at a frequency of 0.0000143 in 1,613,700 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_173854.6 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 3 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SLC41A1 | ENST00000367137.4 | c.1378G>A | p.Ala460Thr | missense_variant | Exon 11 of 11 | 1 | NM_173854.6 | ENSP00000356105.3 | ||
SLC41A1 | ENST00000468057.5 | n.1174G>A | non_coding_transcript_exon_variant | Exon 10 of 10 | 2 | |||||
SLC41A1 | ENST00000484228.1 | n.1444G>A | non_coding_transcript_exon_variant | Exon 3 of 3 | 2 |
Frequencies
GnomAD3 genomes AF: 0.0000197 AC: 3AN: 152024Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000401 AC: 10AN: 249142Hom.: 0 AF XY: 0.0000222 AC XY: 3AN XY: 134898
GnomAD4 exome AF: 0.0000137 AC: 20AN: 1461676Hom.: 0 Cov.: 31 AF XY: 0.00000963 AC XY: 7AN XY: 727134
GnomAD4 genome AF: 0.0000197 AC: 3AN: 152024Hom.: 0 Cov.: 32 AF XY: 0.0000404 AC XY: 3AN XY: 74250
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.1378G>A (p.A460T) alteration is located in exon 11 (coding exon 10) of the SLC41A1 gene. This alteration results from a G to A substitution at nucleotide position 1378, causing the alanine (A) at amino acid position 460 to be replaced by a threonine (T). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at