11-65599612-G-A
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_002419.4(MAP3K11):c.1988C>T(p.Pro663Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000108 in 1,541,604 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_002419.4 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 |
---|---|---|---|---|---|---|---|
MAP3K11 | NM_002419.4 | c.1988C>T | p.Pro663Leu | missense_variant | 9/10 | ENST00000309100.8 | |
MAP3K11 | XM_047426962.1 | c.*67C>T | 3_prime_UTR_variant | 10/10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MAP3K11 | ENST00000309100.8 | c.1988C>T | p.Pro663Leu | missense_variant | 9/10 | 1 | NM_002419.4 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000592 AC: 9AN: 152100Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000768 AC: 12AN: 156222Hom.: 0 AF XY: 0.0000789 AC XY: 7AN XY: 88744
GnomAD4 exome AF: 0.000114 AC: 158AN: 1389504Hom.: 0 Cov.: 34 AF XY: 0.000116 AC XY: 80AN XY: 688172
GnomAD4 genome AF: 0.0000592 AC: 9AN: 152100Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74288
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Mar 16, 2022 | The c.1988C>T (p.P663L) alteration is located in exon 9 (coding exon 9) of the MAP3K11 gene. This alteration results from a C to T substitution at nucleotide position 1988, causing the proline (P) at amino acid position 663 to be replaced by a leucine (L). 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