chr1-110341075-C-T
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_022768.5(RBM15):c.1670C>T(p.Ala557Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000935 in 1,614,170 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 Likely benign (★).
Frequency
Consequence
NM_022768.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -10 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RBM15 | NM_022768.5 | c.1670C>T | p.Ala557Val | missense_variant | 1/3 | ENST00000369784.9 | |
RBM15 | NM_001201545.2 | c.1670C>T | p.Ala557Val | missense_variant | 1/2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RBM15 | ENST00000369784.9 | c.1670C>T | p.Ala557Val | missense_variant | 1/3 | 1 | NM_022768.5 | A2 |
Frequencies
GnomAD3 genomes ? AF: 0.000513 AC: 78AN: 152190Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000175 AC: 44AN: 251390Hom.: 0 AF XY: 0.000103 AC XY: 14AN XY: 135898
GnomAD4 exome AF: 0.0000493 AC: 72AN: 1461862Hom.: 0 Cov.: 34 AF XY: 0.0000399 AC XY: 29AN XY: 727226
GnomAD4 genome ? AF: 0.000519 AC: 79AN: 152308Hom.: 0 Cov.: 32 AF XY: 0.000524 AC XY: 39AN XY: 74486
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jul 17, 2018 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at