NM_001099697.2:c.2540T>C
Variant summary
Our verdict is Likely benign. The variant received -6 ACMG points: 0P and 6B. BP4_StrongBP6_Moderate
The NM_001099697.2(RSPH10B2):c.2540T>C(p.Leu847Pro) variant causes a missense change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. 17/22 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_001099697.2 missense
Scores
Clinical Significance
Conservation
Publications
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ACMG classification
Our verdict: Likely_benign. The variant received -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
RSPH10B2 | NM_001099697.2 | c.2540T>C | p.Leu847Pro | missense_variant | Exon 21 of 21 | ENST00000404077.6 | NP_001093167.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00 AC: 0AN: 64684Hom.: 0 Cov.: 7
GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.00000877 AC: 9AN: 1026732Hom.: 3 Cov.: 17 AF XY: 0.00000591 AC XY: 3AN XY: 507302 show subpopulations
Age Distribution
GnomAD4 genome Data not reliable, filtered out with message: AC0;AS_VQSR AF: 0.00 AC: 0AN: 64684Hom.: 0 Cov.: 7 AF XY: 0.00 AC XY: 0AN XY: 29590
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