1-15660237-T-G
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_006511.3(RSC1A1):āc.369T>Gā(p.Phe123Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000632 in 1,614,056 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 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.369T>G | p.Phe123Leu | missense_variant | 1/1 | ENST00000345034.2 | |
DDI2 | NM_032341.5 | c.*447T>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.369T>G | p.Phe123Leu | missense_variant | 1/1 | NM_006511.3 | P1 | ||
DDI2 | ENST00000480945.6 | c.*447T>G | 3_prime_UTR_variant | 10/10 | 2 | NM_032341.5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000591 AC: 9AN: 152172Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000239 AC: 6AN: 250978Hom.: 0 AF XY: 0.0000147 AC XY: 2AN XY: 135626
GnomAD4 exome AF: 0.0000636 AC: 93AN: 1461884Hom.: 0 Cov.: 32 AF XY: 0.0000674 AC XY: 49AN XY: 727244
GnomAD4 genome ? AF: 0.0000591 AC: 9AN: 152172Hom.: 0 Cov.: 33 AF XY: 0.0000538 AC XY: 4AN XY: 74332
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | May 23, 2023 | The c.369T>G (p.F123L) alteration is located in exon 1 (coding exon 1) of the RSC1A1 gene. This alteration results from a T to G substitution at nucleotide position 369, causing the phenylalanine (F) at amino acid position 123 to be replaced by a leucine (L). 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