chr19-38608030-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001042600.3(MAP4K1):c.1069C>T(p.Arg357Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000706 in 1,600,248 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 16/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001042600.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MAP4K1 | NM_001042600.3 | c.1069C>T | p.Arg357Cys | missense_variant | 15/31 | ENST00000396857.7 | |
MAP4K1 | NM_007181.6 | c.1069C>T | p.Arg357Cys | missense_variant | 15/32 | ||
MAP4K1 | XM_011526404.2 | c.1069C>T | p.Arg357Cys | missense_variant | 15/32 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MAP4K1 | ENST00000396857.7 | c.1069C>T | p.Arg357Cys | missense_variant | 15/31 | 5 | NM_001042600.3 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000132 AC: 2AN: 152010Hom.: 0 Cov.: 30
GnomAD3 exomes AF: 0.0000423 AC: 10AN: 236676Hom.: 0 AF XY: 0.0000311 AC XY: 4AN XY: 128774
GnomAD4 exome AF: 0.0000766 AC: 111AN: 1448238Hom.: 0 Cov.: 33 AF XY: 0.0000681 AC XY: 49AN XY: 719154
GnomAD4 genome AF: 0.0000132 AC: 2AN: 152010Hom.: 0 Cov.: 30 AF XY: 0.0000135 AC XY: 1AN XY: 74252
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 02, 2022 | The c.1069C>T (p.R357C) alteration is located in exon 15 (coding exon 15) of the MAP4K1 gene. This alteration results from a C to T substitution at nucleotide position 1069, causing the arginine (R) at amino acid position 357 to be replaced by a cysteine (C). 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