19-6218013-C-T

Variant summary

Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4

The NM_005934.4(MLLT1):​c.1139G>A​(p.Ser380Asn) variant causes a missense change. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. S380T) has been classified as Uncertain significance.

Frequency

Genomes: not found (cov: 33)

Consequence

MLLT1
NM_005934.4 missense

Scores

12
7

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 4.96
Variant links:
Genes affected
MLLT1 (HGNC:7134): (MLLT1 super elongation complex subunit) Predicted to be involved in regulation of transcription, DNA-templated. Predicted to act upstream of or within negative regulation of protein kinase activity. Located in cytosol; fibrillar center; and nucleoplasm. Part of transcription elongation factor complex. [provided by Alliance of Genome Resources, Apr 2022]

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ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 1 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.39414817).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
MLLT1NM_005934.4 linkc.1139G>A p.Ser380Asn missense_variant Exon 7 of 12 ENST00000252674.9 NP_005925.2 Q03111

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
MLLT1ENST00000252674.9 linkc.1139G>A p.Ser380Asn missense_variant Exon 7 of 12 1 NM_005934.4 ENSP00000252674.6 Q03111

Frequencies

GnomAD3 genomes
Cov.:
33
GnomAD4 exome
Cov.:
31
GnomAD4 genome
Cov.:
33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Uncertain
0.38
BayesDel_addAF
Benign
-0.058
T
BayesDel_noAF
Benign
-0.32
CADD
Uncertain
24
DANN
Uncertain
0.99
DEOGEN2
Uncertain
0.57
D
Eigen
Uncertain
0.66
Eigen_PC
Uncertain
0.61
FATHMM_MKL
Uncertain
0.87
D
LIST_S2
Uncertain
0.91
D
M_CAP
Benign
0.029
D
MetaRNN
Benign
0.39
T
MetaSVM
Uncertain
-0.11
T
MutationAssessor
Uncertain
2.7
M
PrimateAI
Uncertain
0.65
T
PROVEAN
Benign
-2.0
N
REVEL
Benign
0.19
Sift
Uncertain
0.0010
D
Sift4G
Uncertain
0.011
D
Polyphen
0.98
D
Vest4
0.39
MutPred
0.36
Loss of phosphorylation at S380 (P = 2e-04);
MVP
0.57
MPC
0.24
ClinPred
0.90
D
GERP RS
4.6
Varity_R
0.51
gMVP
0.27

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.010
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

No publications associated with this variant yet.

Other links and lift over

hg19: chr19-6218024; API