chr6-44230033-C-G
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BS2
The NM_001372327.1(SLC29A1):c.441C>G(p.Ile147Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000162 in 1,607,780 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts 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. I147T) 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 -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SLC29A1 | NM_001372327.1 | c.441C>G | p.Ile147Met | missense_variant | 5/13 | ENST00000371755.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLC29A1 | ENST00000371755.9 | c.441C>G | p.Ile147Met | missense_variant | 5/13 | 1 | NM_001372327.1 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000118 AC: 18AN: 152188Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000243 AC: 6AN: 246992Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 133834
GnomAD4 exome AF: 0.00000550 AC: 8AN: 1455592Hom.: 0 Cov.: 35 AF XY: 0.00000138 AC XY: 1AN XY: 724328
GnomAD4 genome ? AF: 0.000118 AC: 18AN: 152188Hom.: 0 Cov.: 32 AF XY: 0.0000807 AC XY: 6AN XY: 74352
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 16, 2023 | The c.441C>G (p.I147M) alteration is located in exon 6 (coding exon 4) of the SLC29A1 gene. This alteration results from a C to G substitution at nucleotide position 441, causing the isoleucine (I) at amino acid position 147 to be replaced by a methionine (M). 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