chr7-5287926-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.110C>T(p.Ala37Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000279 in 1,611,648 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 (★). Synonymous variant affecting the same amino acid position (i.e. A37A) has been classified as Likely benign.
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.110C>T | p.Ala37Val | missense_variant | Exon 2 of 11 | ENST00000396872.8 | NP_694979.2 | |
SLC29A4 | NM_001040661.3 | c.110C>T | p.Ala37Val | missense_variant | Exon 2 of 11 | NP_001035751.1 | ||
SLC29A4 | NM_001300847.3 | c.110C>T | p.Ala37Val | missense_variant | Exon 2 of 11 | NP_001287776.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000263 AC: 4AN: 152238Hom.: 0 Cov.: 34
GnomAD3 exomes AF: 0.0000404 AC: 10AN: 247486Hom.: 0 AF XY: 0.0000372 AC XY: 5AN XY: 134546
GnomAD4 exome AF: 0.0000281 AC: 41AN: 1459410Hom.: 0 Cov.: 31 AF XY: 0.0000317 AC XY: 23AN XY: 726018
GnomAD4 genome AF: 0.0000263 AC: 4AN: 152238Hom.: 0 Cov.: 34 AF XY: 0.0000269 AC XY: 2AN XY: 74390
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.110C>T (p.A37V) 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 110, causing the alanine (A) at amino acid position 37 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