chr14-103561082-A-G
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001015048.3(BAG5):c.83T>C(p.Ile28Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000343 in 1,457,914 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 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. I28V) has been classified as Likely benign.
Frequency
Consequence
NM_001015048.3 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 |
---|---|---|---|---|---|---|---|
BAG5 | NM_001015048.3 | c.83T>C | p.Ile28Thr | missense_variant | 2/2 | ENST00000299204.6 | |
BAG5 | NM_001015049.5 | c.83T>C | p.Ile28Thr | missense_variant | 2/2 | ||
BAG5 | NM_004873.4 | c.83T>C | p.Ile28Thr | missense_variant | 2/2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
BAG5 | ENST00000299204.6 | c.83T>C | p.Ile28Thr | missense_variant | 2/2 | 1 | NM_001015048.3 | P1 | |
BAG5 | ENST00000337322.5 | c.83T>C | p.Ile28Thr | missense_variant | 2/2 | 1 | P1 | ||
BAG5 | ENST00000445922.2 | c.83T>C | p.Ile28Thr | missense_variant | 2/2 | 1 | P1 | ||
ENST00000556332.1 | n.443-685A>G | intron_variant, non_coding_transcript_variant | 4 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD3 exomes AF: 0.0000161 AC: 4AN: 248524Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 134694
GnomAD4 exome AF: 0.00000343 AC: 5AN: 1457914Hom.: 0 Cov.: 31 AF XY: 0.00000138 AC XY: 1AN XY: 725526
GnomAD4 genome ? Cov.: 32
ClinVar
Submissions by phenotype
Inborn genetic diseases Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jun 02, 2023 | The c.206T>C (p.I69T) alteration is located in exon 2 (coding exon 2) of the BAG5 gene. This alteration results from a T to C substitution at nucleotide position 206, causing the isoleucine (I) at amino acid position 69 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