X-70928537-A-C
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Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_032803.6(SLC7A3):āc.626T>Gā(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. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: š 0.00025 ( 0 hom., 10 hem., cov: 22)
Exomes š: 0.00011 ( 0 hom. 32 hem. )
Consequence
SLC7A3
NM_032803.6 missense
NM_032803.6 missense
Scores
2
9
6
Clinical Significance
Conservation
PhyloP100: 4.04
Genes affected
SLC7A3 (HGNC:11061): (solute carrier family 7 member 3) This gene encodes a member of the solute carrier family 7. The encoded protein is a sodium-independent cationic amino acid transporter. Alternate splicing results in multiple transcripts that encoded the same protein.[provided by RefSeq, May 2010]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -6 ACMG points.
BP4
Computational evidence support a benign effect (MetaRNN=0.11292094).
BS2
High Hemizygotes in GnomAd4 at 10 gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SLC7A3 | NM_032803.6 | c.626T>G | p.Phe209Cys | missense_variant | 4/12 | ENST00000374299.8 | NP_116192.4 | |
SLC7A3 | NM_001048164.3 | c.626T>G | p.Phe209Cys | missense_variant | 4/12 | NP_001041629.1 | ||
SLC7A3 | XM_047442598.1 | c.626T>G | p.Phe209Cys | missense_variant | 3/11 | XP_047298554.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SLC7A3 | ENST00000374299.8 | c.626T>G | p.Phe209Cys | missense_variant | 4/12 | 1 | NM_032803.6 | ENSP00000363417.3 | ||
SLC7A3 | ENST00000298085.4 | c.626T>G | p.Phe209Cys | missense_variant | 4/12 | 2 | ENSP00000298085.4 |
Frequencies
GnomAD3 genomes AF: 0.000253 AC: 28AN: 110758Hom.: 0 Cov.: 22 AF XY: 0.000303 AC XY: 10AN XY: 32974
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GnomAD3 exomes AF: 0.000229 AC: 39AN: 170335Hom.: 0 AF XY: 0.000177 AC XY: 10AN XY: 56377
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GnomAD4 exome AF: 0.000106 AC: 116AN: 1093639Hom.: 0 Cov.: 32 AF XY: 0.0000890 AC XY: 32AN XY: 359575
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GnomAD4 genome AF: 0.000253 AC: 28AN: 110758Hom.: 0 Cov.: 22 AF XY: 0.000303 AC XY: 10AN XY: 32974
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ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Sep 25, 2024 | 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:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Uncertain
CADD
Benign
DANN
Uncertain
DEOGEN2
Uncertain
D;D
FATHMM_MKL
Uncertain
D
LIST_S2
Uncertain
.;D
M_CAP
Uncertain
D
MetaRNN
Benign
T;T
MetaSVM
Uncertain
D
MutationAssessor
Pathogenic
M;M
PrimateAI
Uncertain
T
PROVEAN
Pathogenic
D;D
REVEL
Uncertain
Sift
Benign
D;D
Sift4G
Benign
T;T
Polyphen
B;B
Vest4
MVP
MPC
ClinPred
T
GERP RS
Varity_R
gMVP
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at