5-36301365-T-C
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_145000.5(RANBP3L):c.52A>G(p.Thr18Ala) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000558 in 1,613,774 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 (★).
Frequency
Consequence
NM_145000.5 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 |
---|---|---|---|---|---|---|---|
RANBP3L | NM_145000.5 | c.52A>G | p.Thr18Ala | missense_variant | 1/14 | ENST00000296604.8 | |
LOC124900962 | XR_007058733.1 | n.128-26279T>C | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RANBP3L | ENST00000296604.8 | c.52A>G | p.Thr18Ala | missense_variant | 1/14 | 1 | NM_145000.5 | A2 | |
RANBP3L | ENST00000502994.5 | c.52A>G | p.Thr18Ala | missense_variant | 1/15 | 2 | P4 | ||
RANBP3L | ENST00000515759.5 | c.52A>G | p.Thr18Ala | missense_variant | 1/10 | 2 | |||
RANBP3L | ENST00000505865.1 | c.52A>G | p.Thr18Ala | missense_variant | 2/6 | 4 |
Frequencies
GnomAD3 genomes ? AF: 0.0000329 AC: 5AN: 152178Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000159 AC: 4AN: 250842Hom.: 0 AF XY: 0.00000738 AC XY: 1AN XY: 135538
GnomAD4 exome AF: 0.00000274 AC: 4AN: 1461478Hom.: 0 Cov.: 31 AF XY: 0.00000275 AC XY: 2AN XY: 727016
GnomAD4 genome ? AF: 0.0000328 AC: 5AN: 152296Hom.: 0 Cov.: 33 AF XY: 0.0000537 AC XY: 4AN XY: 74468
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 02, 2022 | The c.52A>G (p.T18A) alteration is located in exon 1 (coding exon 1) of the RANBP3L gene. This alteration results from a A to G substitution at nucleotide position 52, causing the threonine (T) at amino acid position 18 to be replaced by an alanine (A). 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