5-56875191-G-C
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_005921.2(MAP3K1):āc.1846G>Cā(p.Gly616Arg) variant causes a missense change. The variant allele was found at a frequency of 0.0000149 in 1,614,010 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin ClinVar.
Frequency
Consequence
NM_005921.2 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MAP3K1 | NM_005921.2 | c.1846G>C | p.Gly616Arg | missense_variant | 10/20 | ENST00000399503.4 | |
MAP3K1 | XM_047417218.1 | c.1846G>C | p.Gly616Arg | missense_variant | 10/18 | ||
MAP3K1 | XM_047417219.1 | c.1435G>C | p.Gly479Arg | missense_variant | 11/21 | ||
MAP3K1 | XM_047417220.1 | c.1435G>C | p.Gly479Arg | missense_variant | 11/21 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MAP3K1 | ENST00000399503.4 | c.1846G>C | p.Gly616Arg | missense_variant | 10/20 | 1 | NM_005921.2 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000131 AC: 2AN: 152182Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000161 AC: 4AN: 249150Hom.: 0 AF XY: 0.0000296 AC XY: 4AN XY: 135160
GnomAD4 exome AF: 0.0000150 AC: 22AN: 1461828Hom.: 0 Cov.: 32 AF XY: 0.0000151 AC XY: 11AN XY: 727214
GnomAD4 genome AF: 0.0000131 AC: 2AN: 152182Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74360
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Genetic Services Laboratory, University of Chicago | Feb 24, 2021 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at