chr8-38209121-G-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_004874.4(BAG4):c.742G>A(p.Ala248Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000527 in 1,614,000 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 (★).
Frequency
Consequence
NM_004874.4 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 |
---|---|---|---|---|---|---|---|
BAG4 | NM_004874.4 | c.742G>A | p.Ala248Thr | missense_variant | 4/5 | ENST00000287322.5 | |
BAG4 | NM_001204878.2 | c.634G>A | p.Ala212Thr | missense_variant | 3/4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
BAG4 | ENST00000287322.5 | c.742G>A | p.Ala248Thr | missense_variant | 4/5 | 1 | NM_004874.4 | P1 | |
BAG4 | ENST00000432471.6 | c.634G>A | p.Ala212Thr | missense_variant | 3/4 | 1 | |||
BAG4 | ENST00000521311.1 | c.283G>A | p.Ala95Thr | missense_variant | 2/2 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000592 AC: 9AN: 152116Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000131 AC: 33AN: 251426Hom.: 0 AF XY: 0.000169 AC XY: 23AN XY: 135900
GnomAD4 exome AF: 0.0000520 AC: 76AN: 1461884Hom.: 0 Cov.: 30 AF XY: 0.0000523 AC XY: 38AN XY: 727244
GnomAD4 genome ? AF: 0.0000592 AC: 9AN: 152116Hom.: 0 Cov.: 32 AF XY: 0.0000404 AC XY: 3AN XY: 74294
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 10, 2023 | The c.742G>A (p.A248T) alteration is located in exon 4 (coding exon 4) of the BAG4 gene. This alteration results from a G to A substitution at nucleotide position 742, causing the alanine (A) at amino acid position 248 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