chr10-13192356-A-T
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_018518.5(MCM10):c.1618A>T(p.Thr540Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.142 in 1,613,626 control chromosomes in the GnomAD database, including 18,506 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Consequence
NM_018518.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -12 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
MCM10 | NM_018518.5 | c.1618A>T | p.Thr540Ser | missense_variant | 12/20 | ENST00000378714.8 | NP_060988.3 | |
MCM10 | NM_182751.3 | c.1621A>T | p.Thr541Ser | missense_variant | 12/20 | NP_877428.1 | ||
MCM10 | XM_011519538.3 | c.1621A>T | p.Thr541Ser | missense_variant | 12/20 | XP_011517840.1 | ||
MCM10 | XM_047425437.1 | c.1618A>T | p.Thr540Ser | missense_variant | 12/20 | XP_047281393.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
MCM10 | ENST00000378714.8 | c.1618A>T | p.Thr540Ser | missense_variant | 12/20 | 1 | NM_018518.5 | ENSP00000367986 | P4 | |
MCM10 | ENST00000484800.6 | c.1621A>T | p.Thr541Ser | missense_variant | 12/20 | 1 | ENSP00000418268 | A1 | ||
MCM10 | ENST00000378694.1 | c.1618A>T | p.Thr540Ser | missense_variant | 11/18 | 5 | ENSP00000367966 |
Frequencies
GnomAD3 genomes AF: 0.122 AC: 18592AN: 152012Hom.: 1392 Cov.: 32
GnomAD3 exomes AF: 0.115 AC: 28832AN: 251270Hom.: 2295 AF XY: 0.114 AC XY: 15510AN XY: 135790
GnomAD4 exome AF: 0.144 AC: 210785AN: 1461496Hom.: 17113 Cov.: 32 AF XY: 0.141 AC XY: 102822AN XY: 727084
GnomAD4 genome AF: 0.122 AC: 18610AN: 152130Hom.: 1393 Cov.: 32 AF XY: 0.121 AC XY: 9030AN XY: 74358
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at