7-5291183-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_153247.4(SLC29A4):c.361C>T(p.Leu121Phe) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000731 in 1,613,662 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. L121V) has been classified as Uncertain significance.
Frequency
Consequence
NM_153247.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SLC29A4 | NM_153247.4 | c.361C>T | p.Leu121Phe | missense_variant | Exon 4 of 11 | ENST00000396872.8 | NP_694979.2 | |
SLC29A4 | NM_001040661.3 | c.361C>T | p.Leu121Phe | missense_variant | Exon 4 of 11 | NP_001035751.1 | ||
SLC29A4 | NM_001300847.3 | c.361C>T | p.Leu121Phe | missense_variant | Exon 4 of 11 | NP_001287776.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000657 AC: 10AN: 152180Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000318 AC: 8AN: 251230Hom.: 0 AF XY: 0.0000221 AC XY: 3AN XY: 135868
GnomAD4 exome AF: 0.0000739 AC: 108AN: 1461482Hom.: 0 Cov.: 31 AF XY: 0.0000784 AC XY: 57AN XY: 727022
GnomAD4 genome AF: 0.0000657 AC: 10AN: 152180Hom.: 0 Cov.: 33 AF XY: 0.0000672 AC XY: 5AN XY: 74356
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.361C>T (p.L121F) alteration is located in exon 4 (coding exon 3) of the SLC29A4 gene. This alteration results from a C to T substitution at nucleotide position 361, causing the leucine (L) at amino acid position 121 to be replaced by a phenylalanine (F). 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