19-38605577-C-A
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001042600.3(MAP4K1):c.1354G>T(p.Ala452Ser) variant causes a missense change. The variant allele was found at a frequency of 0.00000217 in 1,383,298 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. A452V) has been classified 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 rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
MAP4K1 | NM_001042600.3 | c.1354G>T | p.Ala452Ser | missense_variant | Exon 18 of 31 | ENST00000396857.7 | NP_001036065.1 | |
MAP4K1 | NM_007181.6 | c.1354G>T | p.Ala452Ser | missense_variant | Exon 18 of 32 | NP_009112.1 | ||
MAP4K1 | XM_011526404.2 | c.1474G>T | p.Ala492Ser | missense_variant | Exon 19 of 32 | XP_011524706.1 |
Ensembl
Frequencies
GnomAD3 genomes Cov.: 31
GnomAD3 exomes AF: 0.00000707 AC: 1AN: 141520Hom.: 0 AF XY: 0.0000129 AC XY: 1AN XY: 77466
GnomAD4 exome AF: 0.00000217 AC: 3AN: 1383298Hom.: 0 Cov.: 34 AF XY: 0.00000293 AC XY: 2AN XY: 683444
GnomAD4 genome Cov.: 31
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.1354G>T (p.A452S) alteration is located in exon 18 (coding exon 18) of the MAP4K1 gene. This alteration results from a G to T substitution at nucleotide position 1354, causing the alanine (A) at amino acid position 452 to be replaced by a serine (S). 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