rs199499379
Variant summary
Our verdict is Likely benign. The variant received -2 ACMG points: 0P and 2B. BP4_Moderate
The NM_001348680.2(SAP25):c.398C>T(p.Thr133Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000171 in 1,508,526 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001348680.2 missense
Scores
Clinical Significance
Conservation
Publications
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ACMG classification
Our verdict: Likely_benign. The variant received -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SAP25 | NM_001348680.2 | c.398C>T | p.Thr133Met | missense_variant | Exon 4 of 6 | ENST00000622764.3 | NP_001335609.1 | |
SAP25 | NM_001168682.3 | c.377C>T | p.Thr126Met | missense_variant | Exon 4 of 6 | NP_001162153.2 | ||
SAP25 | NM_001348677.2 | c.104C>T | p.Thr35Met | missense_variant | Exon 3 of 5 | NP_001335606.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SAP25 | ENST00000622764.3 | c.398C>T | p.Thr133Met | missense_variant | Exon 4 of 6 | 5 | NM_001348680.2 | ENSP00000481773.2 |
Frequencies
GnomAD3 genomes AF: 0.000960 AC: 146AN: 152056Hom.: 0 Cov.: 32 show subpopulations
GnomAD2 exomes AF: 0.000252 AC: 30AN: 119072 AF XY: 0.000174 show subpopulations
GnomAD4 exome AF: 0.0000796 AC: 108AN: 1356352Hom.: 1 Cov.: 32 AF XY: 0.0000585 AC XY: 39AN XY: 666978 show subpopulations
GnomAD4 genome AF: 0.000986 AC: 150AN: 152174Hom.: 0 Cov.: 32 AF XY: 0.000901 AC XY: 67AN XY: 74402 show subpopulations
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.104C>T (p.T35M) alteration is located in exon 4 (coding exon 2) of the SAP25 gene. This alteration results from a C to T substitution at nucleotide position 104, causing the threonine (T) at amino acid position 35 to be replaced by a methionine (M). 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