1-205791555-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_173854.6(SLC41A1):c.1520G>A(p.Arg507Gln) variant causes a missense change. The variant allele was found at a frequency of 0.000101 in 1,613,938 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign 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 0 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SLC41A1 | ENST00000367137.4 | c.1520G>A | p.Arg507Gln | missense_variant | Exon 11 of 11 | 1 | NM_173854.6 | ENSP00000356105.3 | ||
SLC41A1 | ENST00000468057.5 | n.1316G>A | non_coding_transcript_exon_variant | Exon 10 of 10 | 2 | |||||
SLC41A1 | ENST00000484228.1 | n.1586G>A | non_coding_transcript_exon_variant | Exon 3 of 3 | 2 |
Frequencies
GnomAD3 genomes AF: 0.0000526 AC: 8AN: 152064Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000517 AC: 13AN: 251374Hom.: 0 AF XY: 0.0000294 AC XY: 4AN XY: 135878
GnomAD4 exome AF: 0.000106 AC: 155AN: 1461874Hom.: 1 Cov.: 31 AF XY: 0.0000990 AC XY: 72AN XY: 727240
GnomAD4 genome AF: 0.0000526 AC: 8AN: 152064Hom.: 0 Cov.: 32 AF XY: 0.0000539 AC XY: 4AN XY: 74252
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.1520G>A (p.R507Q) 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 1520, causing the arginine (R) at amino acid position 507 to be replaced by a glutamine (Q). 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