chr3-127604987-C-T
Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1
The NM_004526.4(MCM2):c.504C>T(p.Ile168Ile) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.728 in 1,613,788 control chromosomes in the GnomAD database, including 431,880 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_004526.4 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -21 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
MCM2 | NM_004526.4 | c.504C>T | p.Ile168Ile | synonymous_variant | Exon 4 of 16 | ENST00000265056.12 | NP_004517.2 | |
MCM2 | XM_024453531.2 | c.477C>T | p.Ile159Ile | synonymous_variant | Exon 4 of 16 | XP_024309299.1 | ||
MCM2 | NR_073375.2 | n.579C>T | non_coding_transcript_exon_variant | Exon 4 of 16 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.674 AC: 102530AN: 152018Hom.: 35397 Cov.: 33
GnomAD3 exomes AF: 0.685 AC: 171734AN: 250872Hom.: 60110 AF XY: 0.689 AC XY: 93533AN XY: 135666
GnomAD4 exome AF: 0.734 AC: 1072127AN: 1461652Hom.: 396478 Cov.: 85 AF XY: 0.730 AC XY: 531130AN XY: 727114
GnomAD4 genome AF: 0.674 AC: 102565AN: 152136Hom.: 35402 Cov.: 33 AF XY: 0.671 AC XY: 49940AN XY: 74380
ClinVar
Submissions by phenotype
not provided Benign:2
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not specified Benign:1
This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. -
Autosomal dominant nonsyndromic hearing loss 70 Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at