6-161048684-T-C
Variant summary
Our verdict is Benign. Variant got -7 ACMG points: 1P and 8B. PP2BP4_StrongBS2
The NM_005922.4(MAP3K4):c.412T>C(p.Tyr138His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000161 in 1,613,920 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_005922.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -7 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MAP3K4 | NM_005922.4 | c.412T>C | p.Tyr138His | missense_variant | 3/27 | ENST00000392142.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MAP3K4 | ENST00000392142.9 | c.412T>C | p.Tyr138His | missense_variant | 3/27 | 1 | NM_005922.4 | A2 |
Frequencies
GnomAD3 genomes ? AF: 0.000105 AC: 16AN: 152108Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000279 AC: 7AN: 250726Hom.: 0 AF XY: 0.0000221 AC XY: 3AN XY: 135608
GnomAD4 exome AF: 0.00000684 AC: 10AN: 1461694Hom.: 0 Cov.: 32 AF XY: 0.00000825 AC XY: 6AN XY: 727168
GnomAD4 genome ? AF: 0.000105 AC: 16AN: 152226Hom.: 0 Cov.: 32 AF XY: 0.000107 AC XY: 8AN XY: 74430
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jul 08, 2022 | The c.412T>C (p.Y138H) alteration is located in exon 3 (coding exon 3) of the MAP3K4 gene. This alteration results from a T to C substitution at nucleotide position 412, causing the tyrosine (Y) at amino acid position 138 to be replaced by a histidine (H). 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