10-21670478-A-G
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_001195626.3(MLLT10):āc.825A>Gā(p.Ile275Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000118 in 1,613,892 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 (ā ).
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 | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
MLLT10 | NM_001195626.3 | c.825A>G | p.Ile275Met | missense_variant | 10/23 | ENST00000307729.12 | NP_001182555.1 | |
MLLT10 | NM_004641.4 | c.825A>G | p.Ile275Met | missense_variant | 10/24 | NP_004632.1 | ||
MLLT10 | NM_001324297.2 | c.90A>G | p.Ile30Met | missense_variant | 12/25 | NP_001311226.1 | ||
MLLT10 | NR_136736.2 | n.1292A>G | non_coding_transcript_exon_variant | 11/26 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
MLLT10 | ENST00000307729.12 | c.825A>G | p.Ile275Met | missense_variant | 10/23 | 1 | NM_001195626.3 | ENSP00000307411 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000460 AC: 7AN: 152186Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000199 AC: 5AN: 251058Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 135704
GnomAD4 exome AF: 0.00000821 AC: 12AN: 1461706Hom.: 0 Cov.: 30 AF XY: 0.00000413 AC XY: 3AN XY: 727146
GnomAD4 genome AF: 0.0000460 AC: 7AN: 152186Hom.: 0 Cov.: 32 AF XY: 0.0000403 AC XY: 3AN XY: 74358
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Feb 28, 2024 | The c.825A>G (p.I275M) alteration is located in exon 9 (coding exon 9) of the MLLT10 gene. This alteration results from a A to G substitution at nucleotide position 825, causing the isoleucine (I) at amino acid position 275 to be replaced by a methionine (M). 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