chr15-66387346-A-G
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_002755.4(MAP2K1):c.-2A>G variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00867 in 1,559,588 control chromosomes in the GnomAD database, including 194 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_002755.4 5_prime_UTR
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00875 AC: 1331AN: 152092Hom.: 17 Cov.: 32
GnomAD3 exomes AF: 0.0171 AC: 2849AN: 167082Hom.: 86 AF XY: 0.0148 AC XY: 1311AN XY: 88694
GnomAD4 exome AF: 0.00866 AC: 12182AN: 1407378Hom.: 175 Cov.: 32 AF XY: 0.00853 AC XY: 5925AN XY: 695002
GnomAD4 genome AF: 0.00882 AC: 1342AN: 152210Hom.: 19 Cov.: 32 AF XY: 0.00869 AC XY: 647AN XY: 74430
ClinVar
Submissions by phenotype
not specified Benign:6
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not provided Benign:3
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Cardiovascular phenotype Benign:1
This alteration is classified as 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. -
RASopathy Benign:1
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Noonan syndrome and Noonan-related syndrome Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at