X-70928535-C-T
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_ModerateBP6_ModerateBS2
The NM_032803.6(SLC7A3):c.628G>A(p.Val210Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000191 in 1,204,339 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 3 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_032803.6 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 rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SLC7A3 | NM_032803.6 | c.628G>A | p.Val210Ile | missense_variant | Exon 4 of 12 | ENST00000374299.8 | NP_116192.4 | |
SLC7A3 | NM_001048164.3 | c.628G>A | p.Val210Ile | missense_variant | Exon 4 of 12 | NP_001041629.1 | ||
SLC7A3 | XM_047442598.1 | c.628G>A | p.Val210Ile | missense_variant | Exon 3 of 11 | XP_047298554.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000270 AC: 3AN: 111040Hom.: 0 Cov.: 22 AF XY: 0.00 AC XY: 0AN XY: 33234
GnomAD4 exome AF: 0.0000183 AC: 20AN: 1093245Hom.: 0 Cov.: 32 AF XY: 0.00000835 AC XY: 3AN XY: 359279
GnomAD4 genome AF: 0.0000270 AC: 3AN: 111094Hom.: 0 Cov.: 22 AF XY: 0.00 AC XY: 0AN XY: 33298
ClinVar
Submissions by phenotype
not provided Benign:1
SLC7A3: BP4 -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at