chr9-32457241-T-A
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 2P and 10B. PM5BP4_StrongBP6_ModerateBS2
The NM_014314.4(RIGI):c.2659A>T(p.Ile887Leu) variant causes a missense change. The variant allele was found at a frequency of 0.0000564 in 1,614,072 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 (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. I887T) has been classified as Likely pathogenic.
Frequency
Consequence
NM_014314.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RIGI | NM_014314.4 | c.2659A>T | p.Ile887Leu | missense_variant | 18/18 | ENST00000379883.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RIGI | ENST00000379883.3 | c.2659A>T | p.Ile887Leu | missense_variant | 18/18 | 1 | NM_014314.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00000657 AC: 1AN: 152194Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.000131 AC: 33AN: 251456Hom.: 0 AF XY: 0.000169 AC XY: 23AN XY: 135890
GnomAD4 exome AF: 0.0000616 AC: 90AN: 1461878Hom.: 0 Cov.: 32 AF XY: 0.0000811 AC XY: 59AN XY: 727240
GnomAD4 genome ? AF: 0.00000657 AC: 1AN: 152194Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0AN XY: 74364
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Dec 01, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at