5-113043591-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_001085377.2(MCC):c.2695G>A(p.Glu899Lys) variant causes a missense change. The variant allele was found at a frequency of 0.0000533 in 1,614,014 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_001085377.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
MCC | ENST00000408903.7 | c.2695G>A | p.Glu899Lys | missense_variant | Exon 17 of 19 | 2 | NM_001085377.2 | ENSP00000386227.3 | ||
MCC | ENST00000302475.9 | c.2125G>A | p.Glu709Lys | missense_variant | Exon 15 of 17 | 1 | ENSP00000305617.4 | |||
MCC | ENST00000515367.6 | c.1936G>A | p.Glu646Lys | missense_variant | Exon 15 of 17 | 5 | ENSP00000421615.2 |
Frequencies
GnomAD3 genomes AF: 0.0000197 AC: 3AN: 152216Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000398 AC: 10AN: 251292Hom.: 0 AF XY: 0.0000221 AC XY: 3AN XY: 135824
GnomAD4 exome AF: 0.0000568 AC: 83AN: 1461798Hom.: 0 Cov.: 30 AF XY: 0.0000550 AC XY: 40AN XY: 727202
GnomAD4 genome AF: 0.0000197 AC: 3AN: 152216Hom.: 0 Cov.: 33 AF XY: 0.0000403 AC XY: 3AN XY: 74364
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.2695G>A (p.E899K) alteration is located in exon 17 (coding exon 17) of the MCC gene. This alteration results from a G to A substitution at nucleotide position 2695, causing the glutamic acid (E) at amino acid position 899 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