13-29516201-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_003045.5(SLC7A1):c.1723G>A(p.Val575Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000039 in 1,613,570 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 16/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_003045.5 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 |
---|---|---|---|---|---|---|---|---|
SLC7A1 | NM_003045.5 | c.1723G>A | p.Val575Ile | missense_variant | Exon 12 of 13 | ENST00000380752.10 | NP_003036.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000263 AC: 4AN: 152212Hom.: 0 Cov.: 34
GnomAD3 exomes AF: 0.00000799 AC: 2AN: 250422Hom.: 0 AF XY: 0.0000148 AC XY: 2AN XY: 135334
GnomAD4 exome AF: 0.0000404 AC: 59AN: 1461358Hom.: 0 Cov.: 30 AF XY: 0.0000413 AC XY: 30AN XY: 726918
GnomAD4 genome AF: 0.0000263 AC: 4AN: 152212Hom.: 0 Cov.: 34 AF XY: 0.0000403 AC XY: 3AN XY: 74354
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.1723G>A (p.V575I) alteration is located in exon 12 (coding exon 10) of the SLC7A1 gene. This alteration results from a G to A substitution at nucleotide position 1723, causing the valine (V) at amino acid position 575 to be replaced by an isoleucine (I). 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