7-5287923-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_153247.4(SLC29A4):c.107C>T(p.Ala36Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000714 in 1,611,656 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_153247.4 missense
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 rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SLC29A4 | NM_153247.4 | c.107C>T | p.Ala36Val | missense_variant | Exon 2 of 11 | ENST00000396872.8 | NP_694979.2 | |
SLC29A4 | NM_001040661.3 | c.107C>T | p.Ala36Val | missense_variant | Exon 2 of 11 | NP_001035751.1 | ||
SLC29A4 | NM_001300847.3 | c.107C>T | p.Ala36Val | missense_variant | Exon 2 of 11 | NP_001287776.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000309 AC: 47AN: 152240Hom.: 0 Cov.: 34
GnomAD3 exomes AF: 0.0000971 AC: 24AN: 247202Hom.: 0 AF XY: 0.0000818 AC XY: 11AN XY: 134508
GnomAD4 exome AF: 0.0000466 AC: 68AN: 1459416Hom.: 0 Cov.: 31 AF XY: 0.0000358 AC XY: 26AN XY: 726028
GnomAD4 genome AF: 0.000309 AC: 47AN: 152240Hom.: 0 Cov.: 34 AF XY: 0.000336 AC XY: 25AN XY: 74382
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.107C>T (p.A36V) alteration is located in exon 2 (coding exon 1) of the SLC29A4 gene. This alteration results from a C to T substitution at nucleotide position 107, causing the alanine (A) at amino acid position 36 to be replaced by a valine (V). 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