chr4-683232-T-C
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_ModerateBP6_Moderate
The NM_032219.4(SLC49A3):c.1129A>G(p.Thr377Ala) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000136 in 1,612,522 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_032219.4 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/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SLC49A3 | NM_032219.4 | c.1129A>G | p.Thr377Ala | missense_variant | 8/10 | ENST00000322224.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLC49A3 | ENST00000322224.9 | c.1129A>G | p.Thr377Ala | missense_variant | 8/10 | 1 | NM_032219.4 | P4 |
Frequencies
GnomAD3 genomes ? AF: 0.000138 AC: 21AN: 151976Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000766 AC: 19AN: 248028Hom.: 0 AF XY: 0.0000593 AC XY: 8AN XY: 134872
GnomAD4 exome AF: 0.000136 AC: 198AN: 1460546Hom.: 0 Cov.: 33 AF XY: 0.000132 AC XY: 96AN XY: 726580
GnomAD4 genome ? AF: 0.000138 AC: 21AN: 151976Hom.: 0 Cov.: 33 AF XY: 0.000135 AC XY: 10AN XY: 74226
ClinVar
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Nov 29, 2023 | This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at