2-173910024-C-T
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_003111.5(SP3):c.2263G>A(p.Ala755Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000089 in 1,461,436 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_003111.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -10 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SP3 | NM_003111.5 | c.2263G>A | p.Ala755Thr | missense_variant | Exon 7 of 7 | ENST00000310015.12 | NP_003102.1 | |
SP3 | NM_001172712.1 | c.2254G>A | p.Ala752Thr | missense_variant | Exon 7 of 7 | NP_001166183.1 | ||
SP3 | NM_001017371.5 | c.2059G>A | p.Ala687Thr | missense_variant | Exon 5 of 5 | NP_001017371.3 |
Ensembl
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 exomes AF: 0.00000798 AC: 2AN: 250526Hom.: 0 AF XY: 0.00000739 AC XY: 1AN XY: 135382
GnomAD4 exome AF: 0.00000890 AC: 13AN: 1461436Hom.: 0 Cov.: 31 AF XY: 0.0000110 AC XY: 8AN XY: 727002
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
not specified Benign:1
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