NM_032803.6:c.626T>G
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_032803.6(SLC7A3):c.626T>G(p.Phe209Cys) variant causes a missense change. The variant allele was found at a frequency of 0.00012 in 1,204,397 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 42 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_032803.6 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SLC7A3 | NM_032803.6 | c.626T>G | p.Phe209Cys | missense_variant | Exon 4 of 12 | ENST00000374299.8 | NP_116192.4 | |
SLC7A3 | NM_001048164.3 | c.626T>G | p.Phe209Cys | missense_variant | Exon 4 of 12 | NP_001041629.1 | ||
SLC7A3 | XM_047442598.1 | c.626T>G | p.Phe209Cys | missense_variant | Exon 3 of 11 | XP_047298554.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000253 AC: 28AN: 110758Hom.: 0 Cov.: 22 AF XY: 0.000303 AC XY: 10AN XY: 32974
GnomAD3 exomes AF: 0.000229 AC: 39AN: 170335Hom.: 0 AF XY: 0.000177 AC XY: 10AN XY: 56377
GnomAD4 exome AF: 0.000106 AC: 116AN: 1093639Hom.: 0 Cov.: 32 AF XY: 0.0000890 AC XY: 32AN XY: 359575
GnomAD4 genome AF: 0.000253 AC: 28AN: 110758Hom.: 0 Cov.: 22 AF XY: 0.000303 AC XY: 10AN XY: 32974
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.626T>G (p.F209C) alteration is located in exon 4 (coding exon 3) of the SLC7A3 gene. This alteration results from a T to G substitution at nucleotide position 626, causing the phenylalanine (F) at amino acid position 209 to be replaced by a cysteine (C). 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