rs201661705
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_006517.5(SLC16A2):c.265G>A(p.Ala89Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000397 in 1,209,395 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 11 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. 11/18 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. A89P) has been classified as Likely benign.
Frequency
Consequence
NM_006517.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SLC16A2 | NM_006517.5 | c.265G>A | p.Ala89Thr | missense_variant | 1/6 | ENST00000587091.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLC16A2 | ENST00000587091.6 | c.265G>A | p.Ala89Thr | missense_variant | 1/6 | 1 | NM_006517.5 | P1 | |
SLC16A2 | ENST00000636771.1 | c.13G>A | p.Ala5Thr | missense_variant, NMD_transcript_variant | 1/7 | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.0000885 AC: 10AN: 112961Hom.: 0 Cov.: 24 AF XY: 0.0000855 AC XY: 3AN XY: 35101
GnomAD3 exomes AF: 0.000189 AC: 33AN: 174251Hom.: 0 AF XY: 0.000127 AC XY: 8AN XY: 63087
GnomAD4 exome AF: 0.0000337 AC: 37AN: 1096389Hom.: 0 Cov.: 32 AF XY: 0.0000221 AC XY: 8AN XY: 362199
GnomAD4 genome ? AF: 0.0000973 AC: 11AN: 113006Hom.: 0 Cov.: 24 AF XY: 0.0000853 AC XY: 3AN XY: 35156
ClinVar
Submissions by phenotype
Spastic paraplegia Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Oct 03, 2023 | - - |
Inborn genetic diseases Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Jun 12, 2017 | 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. - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Sep 06, 2019 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at