6-136592452-C-T
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP4BS2
The NM_005923.4(MAP3K5):c.3041G>A(p.Arg1014Gln) variant causes a missense change. The variant allele was found at a frequency of 0.0000291 in 1,613,772 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_005923.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
MAP3K5 | ENST00000359015.5 | c.3041G>A | p.Arg1014Gln | missense_variant | Exon 22 of 30 | 1 | NM_005923.4 | ENSP00000351908.4 | ||
MAP3K5 | ENST00000698928.1 | c.3368G>A | p.Arg1123Gln | missense_variant | Exon 23 of 31 | ENSP00000514039.1 |
Frequencies
GnomAD3 genomes AF: 0.0000197 AC: 3AN: 152012Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000119 AC: 3AN: 251246Hom.: 0 AF XY: 0.00000737 AC XY: 1AN XY: 135774
GnomAD4 exome AF: 0.0000301 AC: 44AN: 1461760Hom.: 1 Cov.: 32 AF XY: 0.0000316 AC XY: 23AN XY: 727178
GnomAD4 genome AF: 0.0000197 AC: 3AN: 152012Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74244
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.3041G>A (p.R1014Q) alteration is located in exon 22 (coding exon 22) of the MAP3K5 gene. This alteration results from a G to A substitution at nucleotide position 3041, causing the arginine (R) at amino acid position 1014 to be replaced by a glutamine (Q). 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