14-103562004-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001015049.5(BAG5):c.-120C>T variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000906 in 1,611,004 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_001015049.5 5_prime_UTR
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
BAG5 | NM_001015048.3 | c.-29+612C>T | intron_variant | Intron 1 of 1 | ENST00000299204.6 | NP_001015048.1 | ||
BAG5 | NM_001015049.5 | c.-120C>T | 5_prime_UTR_variant | Exon 1 of 2 | NP_001015049.2 | |||
BAG5 | NM_004873.4 | c.-29+96C>T | intron_variant | Intron 1 of 1 | NP_004864.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
BAG5 | ENST00000337322.5 | c.-120C>T | 5_prime_UTR_variant | Exon 1 of 2 | 1 | ENSP00000338814.5 | ||||
BAG5 | ENST00000299204.6 | c.-29+612C>T | intron_variant | Intron 1 of 1 | 1 | NM_001015048.3 | ENSP00000299204.4 | |||
BAG5 | ENST00000445922.2 | c.-29+96C>T | intron_variant | Intron 1 of 1 | 1 | ENSP00000391713.2 | ||||
KLC1 | ENST00000557172.5 | c.-2+20G>A | intron_variant | Intron 1 of 2 | 4 | ENSP00000450786.1 |
Frequencies
GnomAD3 genomes AF: 0.0000460 AC: 7AN: 152246Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000201 AC: 5AN: 249282Hom.: 0 AF XY: 0.0000296 AC XY: 4AN XY: 135352
GnomAD4 exome AF: 0.0000953 AC: 139AN: 1458758Hom.: 0 Cov.: 30 AF XY: 0.0000909 AC XY: 66AN XY: 725962
GnomAD4 genome AF: 0.0000460 AC: 7AN: 152246Hom.: 0 Cov.: 33 AF XY: 0.0000538 AC XY: 4AN XY: 74382
ClinVar
Submissions by phenotype
Inborn genetic diseases Uncertain:1
The c.4C>T (p.R2C) alteration is located in exon 1 (coding exon 1) of the BAG5 gene. This alteration results from a C to T substitution at nucleotide position 4, causing the arginine (R) at amino acid position 2 to be replaced by a cysteine (C). 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