2-218383101-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_000578.4(SLC11A1):c.149C>T(p.Pro50Leu) variant causes a missense, splice region change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000192 in 1,613,486 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 17/23 in silico tools predict a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_000578.4 missense, splice_region
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SLC11A1 | NM_000578.4 | c.149C>T | p.Pro50Leu | missense_variant, splice_region_variant | 2/15 | ENST00000233202.11 | NP_000569.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SLC11A1 | ENST00000233202.11 | c.149C>T | p.Pro50Leu | missense_variant, splice_region_variant | 2/15 | 1 | NM_000578.4 | ENSP00000233202 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000197 AC: 3AN: 152072Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.0000404 AC: 10AN: 247454Hom.: 0 AF XY: 0.0000373 AC XY: 5AN XY: 134032
GnomAD4 exome AF: 0.0000192 AC: 28AN: 1461296Hom.: 0 Cov.: 31 AF XY: 0.0000179 AC XY: 13AN XY: 726920
GnomAD4 genome AF: 0.0000197 AC: 3AN: 152190Hom.: 0 Cov.: 31 AF XY: 0.0000134 AC XY: 1AN XY: 74438
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 03, 2021 | The c.149C>T (p.P50L) alteration is located in exon 2 (coding exon 2) of the SLC11A1 gene. This alteration results from a C to T substitution at nucleotide position 149, causing the proline (P) at amino acid position 50 to be replaced by a leucine (L). 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