10-21673524-G-C
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_001195626.3(MLLT10):c.1226G>C(p.Gly409Ala) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000549 in 1,613,656 control chromosomes in the GnomAD database, including 2 homozygotes. 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_001195626.3 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 |
---|---|---|---|---|---|---|---|
MLLT10 | NM_001195626.3 | c.1226G>C | p.Gly409Ala | missense_variant | 11/23 | ENST00000307729.12 | |
MLLT10 | NM_004641.4 | c.1226G>C | p.Gly409Ala | missense_variant | 11/24 | ||
MLLT10 | NM_001324297.2 | c.491G>C | p.Gly164Ala | missense_variant | 13/25 | ||
MLLT10 | NR_136736.2 | n.1693G>C | non_coding_transcript_exon_variant | 12/26 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MLLT10 | ENST00000307729.12 | c.1226G>C | p.Gly409Ala | missense_variant | 11/23 | 1 | NM_001195626.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000369 AC: 56AN: 151902Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.000841 AC: 211AN: 250896Hom.: 1 AF XY: 0.000789 AC XY: 107AN XY: 135590
GnomAD4 exome AF: 0.000568 AC: 830AN: 1461636Hom.: 2 Cov.: 35 AF XY: 0.000561 AC XY: 408AN XY: 727110
GnomAD4 genome ? AF: 0.000368 AC: 56AN: 152020Hom.: 0 Cov.: 31 AF XY: 0.000458 AC XY: 34AN XY: 74308
ClinVar
Submissions by phenotype
Acute myeloid leukemia Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Baylor Genetics | Mar 22, 2018 | This variant was determined to be of uncertain significance according to ACMG Guidelines, 2015 [PMID:25741868]. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at