5-113043570-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001085377.2(MCC):c.2716G>A(p.Glu906Lys) variant causes a missense change. The variant allele was found at a frequency of 0.00000205 in 1,461,804 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict 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 0 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
MCC | ENST00000408903.7 | c.2716G>A | p.Glu906Lys | missense_variant | Exon 17 of 19 | 2 | NM_001085377.2 | ENSP00000386227.3 | ||
MCC | ENST00000302475.9 | c.2146G>A | p.Glu716Lys | missense_variant | Exon 15 of 17 | 1 | ENSP00000305617.4 | |||
MCC | ENST00000515367.6 | c.1957G>A | p.Glu653Lys | missense_variant | Exon 15 of 17 | 5 | ENSP00000421615.2 |
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD3 exomes AF: 0.0000119 AC: 3AN: 251252Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 135806
GnomAD4 exome AF: 0.00000205 AC: 3AN: 1461804Hom.: 0 Cov.: 30 AF XY: 0.00000138 AC XY: 1AN XY: 727206
GnomAD4 genome Cov.: 33
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.2716G>A (p.E906K) 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 2716, causing the glutamic acid (E) at amino acid position 906 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