1-15660640-C-G
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_006511.3(RSC1A1):āc.772C>Gā(p.Leu258Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000682 in 1,614,052 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 Uncertain significance (ā ).
Frequency
Consequence
NM_006511.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RSC1A1 | NM_006511.3 | c.772C>G | p.Leu258Val | missense_variant | 1/1 | ENST00000345034.2 | |
DDI2 | NM_032341.5 | c.*850C>G | 3_prime_UTR_variant | 10/10 | ENST00000480945.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RSC1A1 | ENST00000345034.2 | c.772C>G | p.Leu258Val | missense_variant | 1/1 | NM_006511.3 | P1 | ||
DDI2 | ENST00000480945.6 | c.*850C>G | 3_prime_UTR_variant | 10/10 | 2 | NM_032341.5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000394 AC: 6AN: 152218Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000120 AC: 3AN: 250436Hom.: 0 AF XY: 0.0000148 AC XY: 2AN XY: 135376
GnomAD4 exome AF: 0.00000342 AC: 5AN: 1461834Hom.: 0 Cov.: 32 AF XY: 0.00000550 AC XY: 4AN XY: 727210
GnomAD4 genome ? AF: 0.0000394 AC: 6AN: 152218Hom.: 0 Cov.: 33 AF XY: 0.0000403 AC XY: 3AN XY: 74368
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 10, 2023 | The c.772C>G (p.L258V) alteration is located in exon 1 (coding exon 1) of the RSC1A1 gene. This alteration results from a C to G substitution at nucleotide position 772, causing the leucine (L) at amino acid position 258 to be replaced by a valine (V). 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