10-119651626-C-T
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The NM_004281.4(BAG3):c.-50C>T 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 0.0002 in 1,458,480 control chromosomes in the GnomAD database, including 3 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Consequence
NM_004281.4 5_prime_UTR_premature_start_codon_gain
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
BAG3 | NM_004281.4 | c.-50C>T | 5_prime_UTR_premature_start_codon_gain_variant | Exon 1 of 4 | ENST00000369085.8 | NP_004272.2 | ||
BAG3 | NM_004281.4 | c.-50C>T | 5_prime_UTR_variant | Exon 1 of 4 | ENST00000369085.8 | NP_004272.2 | ||
BAG3 | XM_005270287.2 | c.-50C>T | 5_prime_UTR_premature_start_codon_gain_variant | Exon 1 of 4 | XP_005270344.1 | |||
BAG3 | XM_005270287.2 | c.-50C>T | 5_prime_UTR_variant | Exon 1 of 4 | XP_005270344.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
BAG3 | ENST00000369085 | c.-50C>T | 5_prime_UTR_premature_start_codon_gain_variant | Exon 1 of 4 | 1 | NM_004281.4 | ENSP00000358081.4 | |||
BAG3 | ENST00000369085 | c.-50C>T | 5_prime_UTR_variant | Exon 1 of 4 | 1 | NM_004281.4 | ENSP00000358081.4 |
Frequencies
GnomAD3 genomes AF: 0.00101 AC: 154AN: 151872Hom.: 2 Cov.: 33
GnomAD3 exomes AF: 0.000139 AC: 16AN: 115222Hom.: 0 AF XY: 0.000166 AC XY: 11AN XY: 66364
GnomAD4 exome AF: 0.000103 AC: 134AN: 1306500Hom.: 1 Cov.: 30 AF XY: 0.0000933 AC XY: 60AN XY: 643216
GnomAD4 genome AF: 0.00103 AC: 157AN: 151980Hom.: 2 Cov.: 33 AF XY: 0.00105 AC XY: 78AN XY: 74310
ClinVar
Submissions by phenotype
not specified Benign:1
This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at