14-23308865-G-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_004050.5(BCL2L2):c.482G>A(p.Arg161His) variant causes a missense change. The variant allele was found at a frequency of 0.000122 in 1,319,890 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R161P) has been classified as Uncertain significance.
Frequency
Consequence
NM_004050.5 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 |
---|---|---|---|---|---|---|---|
BCL2L2 | NM_004050.5 | c.482G>A | p.Arg161His | missense_variant | 4/4 | ENST00000250405.10 | |
BCL2L2-PABPN1 | NM_001387343.1 | c.432+666G>A | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
BCL2L2 | ENST00000250405.10 | c.482G>A | p.Arg161His | missense_variant | 4/4 | 1 | NM_004050.5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000217 AC: 33AN: 152166Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.000195 AC: 24AN: 123114Hom.: 0 AF XY: 0.0000912 AC XY: 6AN XY: 65774
GnomAD4 exome AF: 0.000110 AC: 128AN: 1167606Hom.: 0 Cov.: 30 AF XY: 0.0000911 AC XY: 51AN XY: 560044
GnomAD4 genome ? AF: 0.000217 AC: 33AN: 152284Hom.: 0 Cov.: 31 AF XY: 0.000161 AC XY: 12AN XY: 74468
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 02, 2021 | The c.482G>A (p.R161H) alteration is located in exon 4 (coding exon 2) of the BCL2L2 gene. This alteration results from a G to A substitution at nucleotide position 482, causing the arginine (R) at amino acid position 161 to be replaced by a histidine (H). 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