6-44230639-A-G
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_001372327.1(SLC29A1):āc.661A>Gā(p.Ile221Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000398 in 1,508,326 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 16/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_001372327.1 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SLC29A1 | NM_001372327.1 | c.661A>G | p.Ile221Val | missense_variant | 7/13 | ENST00000371755.9 | NP_001359256.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SLC29A1 | ENST00000371755.9 | c.661A>G | p.Ile221Val | missense_variant | 7/13 | 1 | NM_001372327.1 | ENSP00000360820 | P1 |
Frequencies
GnomAD3 genomes AF: 0.00000779 AC: 1AN: 128352Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.00000398 AC: 1AN: 251458Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 135910
GnomAD4 exome AF: 0.00000362 AC: 5AN: 1379974Hom.: 0 Cov.: 34 AF XY: 0.00000438 AC XY: 3AN XY: 685438
GnomAD4 genome AF: 0.00000779 AC: 1AN: 128352Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0AN XY: 59970
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Apr 06, 2024 | The c.661A>G (p.I221V) alteration is located in exon 8 (coding exon 6) of the SLC29A1 gene. This alteration results from a A to G substitution at nucleotide position 661, causing the isoleucine (I) at amino acid position 221 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