7-20159016-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_182762.4(MACC1):c.1345G>A(p.Glu449Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000533 in 1,613,868 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_182762.4 missense
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/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MACC1 | NM_182762.4 | c.1345G>A | p.Glu449Lys | missense_variant | 5/7 | ENST00000400331.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MACC1 | ENST00000400331.10 | c.1345G>A | p.Glu449Lys | missense_variant | 5/7 | 2 | NM_182762.4 | P1 | |
MACC1 | ENST00000332878.8 | c.1345G>A | p.Glu449Lys | missense_variant | 3/5 | 1 | P1 | ||
MACC1 | ENST00000589011.1 | c.1345G>A | p.Glu449Lys | missense_variant | 3/5 | 5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000657 AC: 10AN: 152210Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000319 AC: 8AN: 250410Hom.: 0 AF XY: 0.0000295 AC XY: 4AN XY: 135456
GnomAD4 exome AF: 0.0000520 AC: 76AN: 1461658Hom.: 0 Cov.: 33 AF XY: 0.0000591 AC XY: 43AN XY: 727104
GnomAD4 genome ? AF: 0.0000657 AC: 10AN: 152210Hom.: 0 Cov.: 32 AF XY: 0.0000538 AC XY: 4AN XY: 74356
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 12, 2021 | The c.1345G>A (p.E449K) alteration is located in exon 5 (coding exon 2) of the MACC1 gene. This alteration results from a G to A substitution at nucleotide position 1345, causing the glutamic acid (E) at amino acid position 449 to be replaced by a lysine (K). 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