8-103228059-T-C
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_024812.3(BAALC):āc.398T>Cā(p.Met133Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000411 in 1,461,416 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_024812.3 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 | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
BAALC | NM_024812.3 | c.398T>C | p.Met133Thr | missense_variant | 3/3 | ENST00000309982.10 | NP_079088.1 | |
BAALC | NM_001364874.1 | c.503T>C | p.Met168Thr | missense_variant | 4/4 | NP_001351803.1 | ||
BAALC | NM_001024372.2 | c.*66T>C | 3_prime_UTR_variant | 2/2 | NP_001019543.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
BAALC | ENST00000309982.10 | c.398T>C | p.Met133Thr | missense_variant | 3/3 | 1 | NM_024812.3 | ENSP00000312457.5 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 exomes AF: 0.0000280 AC: 7AN: 249868Hom.: 0 AF XY: 0.00000740 AC XY: 1AN XY: 135152
GnomAD4 exome AF: 0.00000411 AC: 6AN: 1461416Hom.: 0 Cov.: 30 AF XY: 0.00000275 AC XY: 2AN XY: 727044
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 08, 2023 | The c.398T>C (p.M133T) alteration is located in exon 3 (coding exon 3) of the BAALC gene. This alteration results from a T to C substitution at nucleotide position 398, causing the methionine (M) at amino acid position 133 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