1-94845281-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001114106.3(SLC44A3):c.889G>A(p.Val297Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000212 in 1,607,146 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001114106.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SLC44A3 | NM_001114106.3 | c.889G>A | p.Val297Met | missense_variant | 9/15 | ENST00000271227.11 | NP_001107578.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SLC44A3 | ENST00000271227.11 | c.889G>A | p.Val297Met | missense_variant | 9/15 | 1 | NM_001114106.3 | ENSP00000271227.6 |
Frequencies
GnomAD3 genomes AF: 0.000138 AC: 21AN: 152218Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000187 AC: 46AN: 245556Hom.: 0 AF XY: 0.000226 AC XY: 30AN XY: 132606
GnomAD4 exome AF: 0.000219 AC: 319AN: 1454928Hom.: 0 Cov.: 30 AF XY: 0.000225 AC XY: 163AN XY: 723350
GnomAD4 genome AF: 0.000138 AC: 21AN: 152218Hom.: 0 Cov.: 32 AF XY: 0.000175 AC XY: 13AN XY: 74370
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Sep 14, 2023 | The c.889G>A (p.V297M) alteration is located in exon 9 (coding exon 9) of the SLC44A3 gene. This alteration results from a G to A substitution at nucleotide position 889, causing the valine (V) at amino acid position 297 to be replaced by a methionine (M). 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