rs7023954
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_002451.4(MTAP):c.166G>A(p.Val56Ile) variant causes a missense change. The variant allele was found at a frequency of 0.407 in 1,605,850 control chromosomes in the GnomAD database, including 136,352 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_002451.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
MTAP | NM_002451.4 | c.166G>A | p.Val56Ile | missense_variant | Exon 3 of 8 | ENST00000644715.2 | NP_002442.2 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.416 AC: 63154AN: 151810Hom.: 13290 Cov.: 31
GnomAD3 exomes AF: 0.397 AC: 98297AN: 247862Hom.: 20353 AF XY: 0.385 AC XY: 51560AN XY: 134030
GnomAD4 exome AF: 0.406 AC: 591018AN: 1453922Hom.: 123052 Cov.: 32 AF XY: 0.400 AC XY: 289460AN XY: 723284
GnomAD4 genome AF: 0.416 AC: 63217AN: 151928Hom.: 13300 Cov.: 31 AF XY: 0.412 AC XY: 30603AN XY: 74238
ClinVar
Submissions by phenotype
Diaphyseal medullary stenosis-bone malignancy syndrome Benign:3
This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. -
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not provided Benign:2
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at