chr15-66387353-C-T
Variant summary
Our verdict is Benign. Variant got -19 ACMG points: 0P and 19B. BP4_ModerateBP6_Very_StrongBP7BS1BS2
The NM_002755.4(MAP2K1):c.6C>T(p.Pro2Pro) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0004 in 1,562,028 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_002755.4 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -19 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000237 AC: 36AN: 152154Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000129 AC: 22AN: 170280Hom.: 0 AF XY: 0.000121 AC XY: 11AN XY: 90536
GnomAD4 exome AF: 0.000418 AC: 589AN: 1409756Hom.: 1 Cov.: 32 AF XY: 0.000388 AC XY: 270AN XY: 696368
GnomAD4 genome AF: 0.000236 AC: 36AN: 152272Hom.: 0 Cov.: 32 AF XY: 0.000188 AC XY: 14AN XY: 74432
ClinVar
Submissions by phenotype
not provided Benign:3
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MAP2K1: BP4, BP7 -
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not specified Benign:2
Pro2Pro in exon 1 of MAP2K1: This variant is not expected to have clinical signi ficance because it does not alter an amino acid residue and it is not located ne ar a splice junction. -
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Cardiovascular phenotype Benign:1
This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. -
Noonan syndrome and Noonan-related syndrome Benign:1
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RASopathy Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at