chr9-20360786-G-A
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_004529.4(MLLT3):c.1387C>T(p.His463Tyr) variant causes a missense change. The variant allele was found at a frequency of 0.00000991 in 1,614,032 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. H463R) has been classified as Uncertain significance.
Frequency
Consequence
NM_004529.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MLLT3 | NM_004529.4 | c.1387C>T | p.His463Tyr | missense_variant | 8/11 | ENST00000380338.9 | |
LOC124902129 | XR_007061434.1 | n.3880-542G>A | intron_variant, non_coding_transcript_variant | ||||
MLLT3 | NM_001286691.2 | c.1378C>T | p.His460Tyr | missense_variant | 8/11 | ||
LOC124902129 | XR_007061433.1 | n.3785-542G>A | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MLLT3 | ENST00000380338.9 | c.1387C>T | p.His463Tyr | missense_variant | 8/11 | 1 | NM_004529.4 | P4 |
Frequencies
GnomAD3 genomes ? AF: 0.0000525 AC: 8AN: 152256Hom.: 0 Cov.: 32
GnomAD4 exome AF: 0.00000547 AC: 8AN: 1461776Hom.: 0 Cov.: 30 AF XY: 0.00000275 AC XY: 2AN XY: 727188
GnomAD4 genome ? AF: 0.0000525 AC: 8AN: 152256Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74392
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Nov 14, 2023 | The c.1387C>T (p.H463Y) alteration is located in exon 8 (coding exon 8) of the MLLT3 gene. This alteration results from a C to T substitution at nucleotide position 1387, causing the histidine (H) at amino acid position 463 to be replaced by a tyrosine (Y). 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