5-56875191-G-A
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_005921.2(MAP3K1):c.1846G>A(p.Gly616Arg) variant causes a missense change. The variant allele was found at a frequency of 0.000994 in 1,614,128 control chromosomes in the GnomAD database, including 2 homozygotes. 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 Likely benign (★★). Another nucleotide change resulting in same amino acid change has been previously reported as Uncertain significancein ClinVar.
Frequency
Consequence
NM_005921.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MAP3K1 | NM_005921.2 | c.1846G>A | p.Gly616Arg | missense_variant | 10/20 | ENST00000399503.4 | |
MAP3K1 | XM_047417218.1 | c.1846G>A | p.Gly616Arg | missense_variant | 10/18 | ||
MAP3K1 | XM_047417219.1 | c.1435G>A | p.Gly479Arg | missense_variant | 11/21 | ||
MAP3K1 | XM_047417220.1 | c.1435G>A | p.Gly479Arg | missense_variant | 11/21 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MAP3K1 | ENST00000399503.4 | c.1846G>A | p.Gly616Arg | missense_variant | 10/20 | 1 | NM_005921.2 | P1 |
Frequencies
GnomAD3 genomes AF: 0.000736 AC: 112AN: 152182Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000610 AC: 152AN: 249150Hom.: 0 AF XY: 0.000651 AC XY: 88AN XY: 135160
GnomAD4 exome AF: 0.00102 AC: 1493AN: 1461828Hom.: 2 Cov.: 32 AF XY: 0.00101 AC XY: 734AN XY: 727214
GnomAD4 genome AF: 0.000735 AC: 112AN: 152300Hom.: 0 Cov.: 32 AF XY: 0.000712 AC XY: 53AN XY: 74488
ClinVar
Submissions by phenotype
46,XY sex reversal 6 Pathogenic:1Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Dec 15, 2023 | - - |
Pathogenic, no assertion criteria provided | literature only | OMIM | Dec 10, 2010 | - - |
Hereditary cancer-predisposing syndrome Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Mendelics | Apr 09, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at