1-15660754-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_006511.3(RSC1A1):c.886C>T(p.Pro296Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000684 in 1,461,352 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_006511.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RSC1A1 | NM_006511.3 | c.886C>T | p.Pro296Ser | missense_variant | 1/1 | ENST00000345034.2 | |
DDI2 | NM_032341.5 | c.*964C>T | 3_prime_UTR_variant | 10/10 | ENST00000480945.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RSC1A1 | ENST00000345034.2 | c.886C>T | p.Pro296Ser | missense_variant | 1/1 | NM_006511.3 | P1 | ||
DDI2 | ENST00000480945.6 | c.*964C>T | 3_prime_UTR_variant | 10/10 | 2 | NM_032341.5 | P1 |
Frequencies
GnomAD3 genomes ? Cov.: 33
GnomAD3 exomes AF: 0.00000399 AC: 1AN: 250466Hom.: 0 AF XY: 0.00000738 AC XY: 1AN XY: 135428
GnomAD4 exome AF: 6.84e-7 AC: 1AN: 1461352Hom.: 0 Cov.: 32 AF XY: 0.00000138 AC XY: 1AN XY: 726944
GnomAD4 genome ? Cov.: 33
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 17, 2024 | The c.886C>T (p.P296S) alteration is located in exon 1 (coding exon 1) of the RSC1A1 gene. This alteration results from a C to T substitution at nucleotide position 886, causing the proline (P) at amino acid position 296 to be replaced by a serine (S). 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