1-15660241-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.373C>T(p.Leu125Phe) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000378 in 1,614,198 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/21 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.373C>T | p.Leu125Phe | missense_variant | 1/1 | ENST00000345034.2 | |
DDI2 | NM_032341.5 | c.*451C>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.373C>T | p.Leu125Phe | missense_variant | 1/1 | NM_006511.3 | P1 | ||
DDI2 | ENST00000480945.6 | c.*451C>T | 3_prime_UTR_variant | 10/10 | 2 | NM_032341.5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000526 AC: 8AN: 152198Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000398 AC: 10AN: 250962Hom.: 0 AF XY: 0.0000369 AC XY: 5AN XY: 135622
GnomAD4 exome AF: 0.0000356 AC: 52AN: 1461882Hom.: 0 Cov.: 32 AF XY: 0.0000316 AC XY: 23AN XY: 727242
GnomAD4 genome ? AF: 0.0000591 AC: 9AN: 152316Hom.: 0 Cov.: 33 AF XY: 0.0000537 AC XY: 4AN XY: 74474
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jul 21, 2021 | The c.373C>T (p.L125F) 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 373, causing the leucine (L) at amino acid position 125 to be replaced by a phenylalanine (F). 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