chr9-4826920-G-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_005772.5(RCL1):c.271G>A(p.Val91Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000836 in 1,614,062 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_005772.5 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 |
---|---|---|---|---|---|---|---|
RCL1 | NM_005772.5 | c.271G>A | p.Val91Ile | missense_variant | 3/9 | ENST00000381750.9 | |
RCL1 | NM_001286699.2 | c.-90-6234G>A | intron_variant | ||||
RCL1 | NM_001286700.2 | c.-91+3301G>A | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RCL1 | ENST00000381750.9 | c.271G>A | p.Val91Ile | missense_variant | 3/9 | 1 | NM_005772.5 | P1 | |
RCL1 | ENST00000381732.3 | c.271G>A | p.Val91Ile | missense_variant | 3/3 | 2 | |||
RCL1 | ENST00000442869.5 | c.-91+3301G>A | intron_variant | 3 | |||||
RCL1 | ENST00000473230.1 | n.213+3301G>A | intron_variant, non_coding_transcript_variant | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.000197 AC: 30AN: 152122Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000954 AC: 24AN: 251476Hom.: 0 AF XY: 0.0000736 AC XY: 10AN XY: 135912
GnomAD4 exome AF: 0.0000718 AC: 105AN: 1461822Hom.: 0 Cov.: 31 AF XY: 0.0000688 AC XY: 50AN XY: 727226
GnomAD4 genome ? AF: 0.000197 AC: 30AN: 152240Hom.: 0 Cov.: 32 AF XY: 0.000228 AC XY: 17AN XY: 74436
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Feb 26, 2024 | The c.271G>A (p.V91I) alteration is located in exon 3 (coding exon 3) of the RCL1 gene. This alteration results from a G to A substitution at nucleotide position 271, causing the valine (V) at amino acid position 91 to be replaced by an isoleucine (I). 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