9-20413813-A-G
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_004529.4(MLLT3):c.1033T>C(p.Ser345Pro) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000279 in 1,613,904 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_004529.4 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 |
---|---|---|---|---|---|---|---|
MLLT3 | NM_004529.4 | c.1033T>C | p.Ser345Pro | missense_variant | 5/11 | ENST00000380338.9 | |
MLLT3 | NM_001286691.2 | c.1024T>C | p.Ser342Pro | missense_variant | 5/11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MLLT3 | ENST00000380338.9 | c.1033T>C | p.Ser345Pro | missense_variant | 5/11 | 1 | NM_004529.4 | P4 | |
MLLT3 | ENST00000630269.2 | c.1024T>C | p.Ser342Pro | missense_variant | 5/11 | 2 | A1 | ||
MLLT3 | ENST00000475957.1 | n.990T>C | non_coding_transcript_exon_variant | 3/5 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.000184 AC: 28AN: 152224Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000518 AC: 13AN: 251164Hom.: 0 AF XY: 0.0000221 AC XY: 3AN XY: 135764
GnomAD4 exome AF: 0.0000116 AC: 17AN: 1461680Hom.: 0 Cov.: 32 AF XY: 0.00000688 AC XY: 5AN XY: 727142
GnomAD4 genome ? AF: 0.000184 AC: 28AN: 152224Hom.: 0 Cov.: 32 AF XY: 0.000161 AC XY: 12AN XY: 74358
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 26, 2022 | The c.1033T>C (p.S345P) alteration is located in exon 5 (coding exon 5) of the MLLT3 gene. This alteration results from a T to C substitution at nucleotide position 1033, causing the serine (S) at amino acid position 345 to be replaced by a proline (P). 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