1-48759164-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001302082.2(BEND5):c.-27G>A variant causes a 5 prime UTR premature start codon gain change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000124 in 1,614,196 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 (★).
Frequency
Consequence
NM_001302082.2 5_prime_UTR_premature_start_codon_gain
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 rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
BEND5 | NM_024603.4 | c.481G>A | p.Val161Met | missense_variant | Exon 3 of 6 | ENST00000371833.4 | NP_078879.2 | |
AGBL4 | NM_032785.4 | c.635-95923G>A | intron_variant | Intron 6 of 13 | ENST00000371839.6 | NP_116174.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
BEND5 | ENST00000371833.4 | c.481G>A | p.Val161Met | missense_variant | Exon 3 of 6 | 1 | NM_024603.4 | ENSP00000360899.3 | ||
AGBL4 | ENST00000371839.6 | c.635-95923G>A | intron_variant | Intron 6 of 13 | 2 | NM_032785.4 | ENSP00000360905.1 |
Frequencies
GnomAD3 genomes AF: 0.0000263 AC: 4AN: 152242Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000160 AC: 4AN: 250676Hom.: 0 AF XY: 0.0000148 AC XY: 2AN XY: 135530
GnomAD4 exome AF: 0.0000109 AC: 16AN: 1461836Hom.: 0 Cov.: 33 AF XY: 0.0000138 AC XY: 10AN XY: 727226
GnomAD4 genome AF: 0.0000263 AC: 4AN: 152360Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 74500
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.481G>A (p.V161M) alteration is located in exon 3 (coding exon 3) of the BEND5 gene. This alteration results from a G to A substitution at nucleotide position 481, causing the valine (V) at amino acid position 161 to be replaced by a methionine (M). 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