chr1-75251260-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001130058.2(SLC44A5):c.295C>T(p.Arg99Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000886 in 1,613,330 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001130058.2 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 | UniProt |
---|---|---|---|---|---|---|---|
SLC44A5 | NM_001130058.2 | c.295C>T | p.Arg99Cys | missense_variant | 7/24 | ENST00000370859.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLC44A5 | ENST00000370859.8 | c.295C>T | p.Arg99Cys | missense_variant | 7/24 | 2 | NM_001130058.2 | A1 | |
SLC44A5 | ENST00000370855.5 | c.295C>T | p.Arg99Cys | missense_variant | 7/24 | 1 | P4 | ||
SLC44A5 | ENST00000469525.1 | n.579C>T | non_coding_transcript_exon_variant | 9/10 | 5 |
Frequencies
GnomAD3 genomes AF: 0.0000723 AC: 11AN: 152134Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000598 AC: 15AN: 250916Hom.: 0 AF XY: 0.0000590 AC XY: 8AN XY: 135592
GnomAD4 exome AF: 0.0000897 AC: 131AN: 1461078Hom.: 0 Cov.: 32 AF XY: 0.0000798 AC XY: 58AN XY: 726864
GnomAD4 genome AF: 0.0000788 AC: 12AN: 152252Hom.: 0 Cov.: 32 AF XY: 0.000107 AC XY: 8AN XY: 74440
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | May 16, 2023 | The c.295C>T (p.R99C) alteration is located in exon 7 (coding exon 6) of the SLC44A5 gene. This alteration results from a C to T substitution at nucleotide position 295, causing the arginine (R) at amino acid position 99 to be replaced by a cysteine (C). 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