chrX-18174125-C-G
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_153346.5(BEND2):āc.1886G>Cā(p.Arg629Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000967 in 1,209,973 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 33 hemizygotes 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 (ā ).
Frequency
Consequence
NM_153346.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
BEND2 | NM_153346.5 | c.1886G>C | p.Arg629Thr | missense_variant | 12/14 | ENST00000380033.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
BEND2 | ENST00000380033.9 | c.1886G>C | p.Arg629Thr | missense_variant | 12/14 | 1 | NM_153346.5 | P1 | |
BEND2 | ENST00000380030.4 | c.1613G>C | p.Arg538Thr | missense_variant | 10/11 | 1 |
Frequencies
GnomAD3 genomes AF: 0.000125 AC: 14AN: 112123Hom.: 0 Cov.: 22 AF XY: 0.0000583 AC XY: 2AN XY: 34287
GnomAD3 exomes AF: 0.0000273 AC: 5AN: 183256Hom.: 0 AF XY: 0.0000148 AC XY: 1AN XY: 67778
GnomAD4 exome AF: 0.0000938 AC: 103AN: 1097850Hom.: 0 Cov.: 31 AF XY: 0.0000853 AC XY: 31AN XY: 363234
GnomAD4 genome AF: 0.000125 AC: 14AN: 112123Hom.: 0 Cov.: 22 AF XY: 0.0000583 AC XY: 2AN XY: 34287
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | May 17, 2023 | The c.1886G>C (p.R629T) alteration is located in exon 12 (coding exon 12) of the BEND2 gene. This alteration results from a G to C substitution at nucleotide position 1886, causing the arginine (R) at amino acid position 629 to be replaced by a threonine (T). 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