X-54440443-G-C
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_058163.3(TSR2):c.22G>C(p.Ala8Pro) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000185 in 1,127,308 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 54 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. 13/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★★).
Frequency
Consequence
NM_058163.3 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 |
---|---|---|---|---|---|---|---|---|
TSR2 | NM_058163.3 | c.22G>C | p.Ala8Pro | missense_variant | Exon 1 of 5 | ENST00000375151.5 | NP_477511.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000978 AC: 11AN: 112508Hom.: 0 Cov.: 23 AF XY: 0.000144 AC XY: 5AN XY: 34640
GnomAD3 exomes AF: 0.0000470 AC: 4AN: 85108Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 14726
GnomAD4 exome AF: 0.000194 AC: 197AN: 1014800Hom.: 0 Cov.: 30 AF XY: 0.000153 AC XY: 49AN XY: 319730
GnomAD4 genome AF: 0.0000978 AC: 11AN: 112508Hom.: 0 Cov.: 23 AF XY: 0.000144 AC XY: 5AN XY: 34640
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.22G>C (p.A8P) alteration is located in exon 1 (coding exon 1) of the TSR2 gene. This alteration results from a G to C substitution at nucleotide position 22, causing the alanine (A) at amino acid position 8 to be replaced by a proline (P). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -
not provided Uncertain:1
This sequence change replaces alanine, which is neutral and non-polar, with proline, which is neutral and non-polar, at codon 8 of the TSR2 protein (p.Ala8Pro). This variant is present in population databases (rs377577583, gnomAD 0.008%). This variant has not been reported in the literature in individuals affected with TSR2-related conditions. ClinVar contains an entry for this variant (Variation ID: 2262503). An algorithm developed to predict the effect of missense changes on protein structure and function (PolyPhen-2) suggests that this variant is likely to be tolerated. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at