6-44230032-T-C
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 1P and 4B. PP3BS2
The NM_001372327.1(SLC29A1):āc.440T>Cā(p.Ile147Thr) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.000018 in 1,607,856 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. I147M) has been classified as Uncertain significance.
Frequency
Consequence
NM_001372327.1 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SLC29A1 | NM_001372327.1 | c.440T>C | p.Ile147Thr | missense_variant | 5/13 | ENST00000371755.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLC29A1 | ENST00000371755.9 | c.440T>C | p.Ile147Thr | missense_variant | 5/13 | 1 | NM_001372327.1 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000986 AC: 15AN: 152184Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000324 AC: 8AN: 247030Hom.: 0 AF XY: 0.0000149 AC XY: 2AN XY: 133858
GnomAD4 exome AF: 0.00000962 AC: 14AN: 1455672Hom.: 0 Cov.: 35 AF XY: 0.00000828 AC XY: 6AN XY: 724372
GnomAD4 genome AF: 0.0000986 AC: 15AN: 152184Hom.: 0 Cov.: 32 AF XY: 0.000135 AC XY: 10AN XY: 74348
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Feb 22, 2023 | The c.440T>C (p.I147T) alteration is located in exon 6 (coding exon 4) of the SLC29A1 gene. This alteration results from a T to C substitution at nucleotide position 440, causing the isoleucine (I) at amino acid position 147 to be replaced by a threonine (T). 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