chr22-43133213-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_173467.5(MCAT):c.1003G>A(p.Glu335Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000235 in 1,614,174 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_173467.5 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 |
---|---|---|---|---|---|---|---|
MCAT | NM_173467.5 | c.1003G>A | p.Glu335Lys | missense_variant | 4/4 | ENST00000290429.11 | |
MCAT | NM_014507.3 | c.*242G>A | 3_prime_UTR_variant | 3/3 | |||
MCAT | NR_046423.1 | n.868G>A | non_coding_transcript_exon_variant | 3/3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MCAT | ENST00000290429.11 | c.1003G>A | p.Glu335Lys | missense_variant | 4/4 | 1 | NM_173467.5 | P1 | |
MCAT | ENST00000327555.5 | c.*242G>A | 3_prime_UTR_variant | 3/3 | 1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000394 AC: 6AN: 152172Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000437 AC: 11AN: 251486Hom.: 0 AF XY: 0.0000515 AC XY: 7AN XY: 135918
GnomAD4 exome AF: 0.0000219 AC: 32AN: 1461884Hom.: 0 Cov.: 62 AF XY: 0.0000275 AC XY: 20AN XY: 727248
GnomAD4 genome ? AF: 0.0000394 AC: 6AN: 152290Hom.: 0 Cov.: 33 AF XY: 0.0000403 AC XY: 3AN XY: 74460
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 28, 2023 | The c.1003G>A (p.E335K) alteration is located in exon 4 (coding exon 4) of the MCAT gene. This alteration results from a G to A substitution at nucleotide position 1003, causing the glutamic acid (E) at amino acid position 335 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