X-18174117-T-A
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_153346.5(BEND2):c.1894A>T(p.Arg632Trp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000248 in 1,209,990 control chromosomes in the GnomAD database, with no homozygous occurrence. There are no hemizygote samples in GnomAD. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict 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. R632K) has been classified as Uncertain significance.
Frequency
Consequence
NM_153346.5 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 |
---|---|---|---|---|---|---|---|
BEND2 | NM_153346.5 | c.1894A>T | p.Arg632Trp | missense_variant | 12/14 | ENST00000380033.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
BEND2 | ENST00000380033.9 | c.1894A>T | p.Arg632Trp | missense_variant | 12/14 | 1 | NM_153346.5 | P1 | |
BEND2 | ENST00000380030.4 | c.1621A>T | p.Arg541Trp | missense_variant | 10/11 | 1 |
Frequencies
GnomAD3 genomes AF: 0.00000892 AC: 1AN: 112170Hom.: 0 Cov.: 23 AF XY: 0.00 AC XY: 0AN XY: 34300
GnomAD4 exome AF: 0.00000182 AC: 2AN: 1097820Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0AN XY: 363196
GnomAD4 genome AF: 0.00000892 AC: 1AN: 112170Hom.: 0 Cov.: 23 AF XY: 0.00 AC XY: 0AN XY: 34300
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Feb 12, 2024 | The c.1894A>T (p.R632W) alteration is located in exon 12 (coding exon 12) of the BEND2 gene. This alteration results from a A to T substitution at nucleotide position 1894, causing the arginine (R) at amino acid position 632 to be replaced by a tryptophan (W). 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