rs766805198
Variant summary
Our verdict is Likely benign. Variant got -1 ACMG points: 3P and 4B. PM2PP2BP4_Strong
The NM_003954.5(MAP3K14):āc.916T>Cā(p.Cys306Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000453 in 1,610,212 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/15 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ). Synonymous variant affecting the same amino acid position (i.e. C306C) has been classified as Likely benign.
Frequency
Consequence
NM_003954.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MAP3K14 | NM_003954.5 | c.916T>C | p.Cys306Arg | missense_variant | 5/16 | ENST00000344686.8 | |
MAP3K14 | XM_047436997.1 | c.916T>C | p.Cys306Arg | missense_variant | 5/15 | ||
MAP3K14 | XM_047436998.1 | c.916T>C | p.Cys306Arg | missense_variant | 6/16 | ||
MAP3K14 | XM_011525441.3 | c.916T>C | p.Cys306Arg | missense_variant | 6/17 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MAP3K14 | ENST00000344686.8 | c.916T>C | p.Cys306Arg | missense_variant | 5/16 | 1 | NM_003954.5 | P1 | |
MAP3K14 | ENST00000376926.8 | c.916T>C | p.Cys306Arg | missense_variant | 4/15 | 1 | P1 | ||
MAP3K14 | ENST00000617331.3 | c.916T>C | p.Cys306Arg | missense_variant | 6/17 | 5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00000658 AC: 1AN: 152084Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000124 AC: 3AN: 241498Hom.: 0 AF XY: 0.0000152 AC XY: 2AN XY: 131166
GnomAD4 exome AF: 0.0000494 AC: 72AN: 1458128Hom.: 0 Cov.: 32 AF XY: 0.0000400 AC XY: 29AN XY: 724918
GnomAD4 genome ? AF: 0.00000658 AC: 1AN: 152084Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74288
ClinVar
Submissions by phenotype
NIK deficiency Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Invitae | Aug 06, 2022 | In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. ClinVar contains an entry for this variant (Variation ID: 544323). This variant has not been reported in the literature in individuals affected with MAP3K14-related conditions. This variant is present in population databases (rs766805198, gnomAD 0.003%). This sequence change replaces cysteine, which is neutral and slightly polar, with arginine, which is basic and polar, at codon 306 of the MAP3K14 protein (p.Cys306Arg). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at