chr5-36271302-A-G
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_145000.5(RANBP3L):c.101T>C(p.Val34Ala) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000279 in 1,431,300 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/21 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 Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RANBP3L | NM_145000.5 | c.101T>C | p.Val34Ala | missense_variant | 2/14 | ENST00000296604.8 | |
LOC124900962 | XR_007058733.1 | n.127+29274A>G | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RANBP3L | ENST00000296604.8 | c.101T>C | p.Val34Ala | missense_variant | 2/14 | 1 | NM_145000.5 | A2 | |
RANBP3L | ENST00000502994.5 | c.101T>C | p.Val34Ala | missense_variant | 2/15 | 2 | P4 | ||
RANBP3L | ENST00000515759.5 | c.101T>C | p.Val34Ala | missense_variant | 2/10 | 2 | |||
RANBP3L | ENST00000505865.1 | c.101T>C | p.Val34Ala | missense_variant | 3/6 | 4 |
Frequencies
GnomAD3 genomes ? Cov.: 33
GnomAD3 exomes AF: 0.0000121 AC: 3AN: 248576Hom.: 0 AF XY: 0.0000149 AC XY: 2AN XY: 134486
GnomAD4 exome AF: 0.00000279 AC: 4AN: 1431300Hom.: 0 Cov.: 26 AF XY: 0.00000420 AC XY: 3AN XY: 713766
GnomAD4 genome ? Cov.: 33
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jun 27, 2022 | The c.101T>C (p.V34A) alteration is located in exon 2 (coding exon 2) of the RANBP3L gene. This alteration results from a T to C substitution at nucleotide position 101, causing the valine (V) at amino acid position 34 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