11-118519367-A-C

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_001197104.2(KMT2A):​c.11147-251A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.082 in 420,912 control chromosomes in the GnomAD database, including 2,352 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.11 ( 1495 hom., cov: 31)
Exomes 𝑓: 0.067 ( 857 hom. )

Consequence

KMT2A
NM_001197104.2 intron

Scores

2

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: -2.00
Variant links:
Genes affected
KMT2A (HGNC:7132): (lysine methyltransferase 2A) This gene encodes a transcriptional coactivator that plays an essential role in regulating gene expression during early development and hematopoiesis. The encoded protein contains multiple conserved functional domains. One of these domains, the SET domain, is responsible for its histone H3 lysine 4 (H3K4) methyltransferase activity which mediates chromatin modifications associated with epigenetic transcriptional activation. This protein is processed by the enzyme Taspase 1 into two fragments, MLL-C and MLL-N. These fragments reassociate and further assemble into different multiprotein complexes that regulate the transcription of specific target genes, including many of the HOX genes. Multiple chromosomal translocations involving this gene are the cause of certain acute lymphoid leukemias and acute myeloid leukemias. Alternate splicing results in multiple transcript variants.[provided by RefSeq, Oct 2010]
TTC36-AS1 (HGNC:55495): (TTC36 and KMT2A antisense RNA 1)

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.9).
BP6
Variant 11-118519367-A-C is Benign according to our data. Variant chr11-118519367-A-C is described in ClinVar as [Benign]. Clinvar id is 1179536.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.237 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
KMT2ANM_001197104.2 linkuse as main transcriptc.11147-251A>C intron_variant ENST00000534358.8
TTC36-AS1NR_120574.1 linkuse as main transcriptn.321+1899T>G intron_variant, non_coding_transcript_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
KMT2AENST00000534358.8 linkuse as main transcriptc.11147-251A>C intron_variant 1 NM_001197104.2 P4Q03164-3
TTC36-AS1ENST00000532597.6 linkuse as main transcriptn.241+1899T>G intron_variant, non_coding_transcript_variant 2

Frequencies

GnomAD3 genomes
AF:
0.109
AC:
16589
AN:
152074
Hom.:
1488
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.241
Gnomad AMI
AF:
0.00330
Gnomad AMR
AF:
0.0563
Gnomad ASJ
AF:
0.0539
Gnomad EAS
AF:
0.0210
Gnomad SAS
AF:
0.0746
Gnomad FIN
AF:
0.0818
Gnomad MID
AF:
0.0475
Gnomad NFE
AF:
0.0599
Gnomad OTH
AF:
0.0808
GnomAD4 exome
AF:
0.0665
AC:
17878
AN:
268720
Hom.:
857
Cov.:
2
AF XY:
0.0662
AC XY:
9188
AN XY:
138750
show subpopulations
Gnomad4 AFR exome
AF:
0.245
Gnomad4 AMR exome
AF:
0.0447
Gnomad4 ASJ exome
AF:
0.0575
Gnomad4 EAS exome
AF:
0.0306
Gnomad4 SAS exome
AF:
0.0788
Gnomad4 FIN exome
AF:
0.0631
Gnomad4 NFE exome
AF:
0.0608
Gnomad4 OTH exome
AF:
0.0749
GnomAD4 genome
AF:
0.109
AC:
16622
AN:
152192
Hom.:
1495
Cov.:
31
AF XY:
0.108
AC XY:
8014
AN XY:
74430
show subpopulations
Gnomad4 AFR
AF:
0.241
Gnomad4 AMR
AF:
0.0562
Gnomad4 ASJ
AF:
0.0539
Gnomad4 EAS
AF:
0.0212
Gnomad4 SAS
AF:
0.0748
Gnomad4 FIN
AF:
0.0818
Gnomad4 NFE
AF:
0.0599
Gnomad4 OTH
AF:
0.0799
Alfa
AF:
0.0783
Hom.:
139
Bravo
AF:
0.114
Asia WGS
AF:
0.0550
AC:
192
AN:
3478

ClinVar

Significance: Benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link

Submissions by phenotype

not provided Benign:2
Benign, criteria provided, single submitterclinical testingGeneDxAug 10, 2018- -
Benign, criteria provided, single submitternot providedBreakthrough Genomics, Breakthrough Genomics-- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.90
CADD
Benign
0.15
DANN
Benign
0.70

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs9332858; hg19: chr11-118390082; COSMIC: COSV104417806; COSMIC: COSV104417806; API