8-103212981-C-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_024812.3(BAALC):c.223C>A(p.Pro75Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000018 in 1,614,140 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
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.223C>A | p.Pro75Thr | missense_variant | 2/3 | ENST00000309982.10 | NP_079088.1 | |
BAALC | NM_001364874.1 | c.328C>A | p.Pro110Thr | missense_variant | 3/4 | NP_001351803.1 | ||
BAALC | NM_001024372.2 | c.161-15008C>A | intron_variant | NP_001019543.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
BAALC | ENST00000309982.10 | c.223C>A | p.Pro75Thr | missense_variant | 2/3 | 1 | NM_024812.3 | ENSP00000312457.5 |
Frequencies
GnomAD3 genomes AF: 0.0000394 AC: 6AN: 152198Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000597 AC: 15AN: 251234Hom.: 0 AF XY: 0.0000589 AC XY: 8AN XY: 135758
GnomAD4 exome AF: 0.0000157 AC: 23AN: 1461824Hom.: 0 Cov.: 30 AF XY: 0.0000138 AC XY: 10AN XY: 727214
GnomAD4 genome AF: 0.0000394 AC: 6AN: 152316Hom.: 0 Cov.: 32 AF XY: 0.0000403 AC XY: 3AN XY: 74482
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Nov 29, 2021 | The c.223C>A (p.P75T) alteration is located in exon 2 (coding exon 2) of the BAALC gene. This alteration results from a C to A substitution at nucleotide position 223, causing the proline (P) at amino acid position 75 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