chr2-135852855-T-C
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_005915.6(MCM6):c.1687A>G(p.Ile563Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000602 in 1,611,332 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_005915.6 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MCM6 | NM_005915.6 | c.1687A>G | p.Ile563Val | missense_variant | 12/17 | ENST00000264156.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MCM6 | ENST00000264156.3 | c.1687A>G | p.Ile563Val | missense_variant | 12/17 | 1 | NM_005915.6 | P1 | |
MCM6 | ENST00000492091.1 | n.182-1292A>G | intron_variant, non_coding_transcript_variant | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.0000131 AC: 2AN: 152222Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000116 AC: 29AN: 248954Hom.: 0 AF XY: 0.000111 AC XY: 15AN XY: 134684
GnomAD4 exome AF: 0.0000651 AC: 95AN: 1459110Hom.: 0 Cov.: 29 AF XY: 0.0000813 AC XY: 59AN XY: 725956
GnomAD4 genome ? AF: 0.0000131 AC: 2AN: 152222Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74366
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 12, 2021 | The c.1687A>G (p.I563V) alteration is located in exon 12 (coding exon 12) of the MCM6 gene. This alteration results from a A to G substitution at nucleotide position 1687, causing the isoleucine (I) at amino acid position 563 to be replaced by a valine (V). 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