rs587781999
Positions:
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The variant allele was found at a frequency of 0.0000242 in 662,080 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: 𝑓 0.000039 ( 0 hom., cov: 33)
Exomes 𝑓: 0.000020 ( 0 hom. )
Consequence
Unknown
Scores
2
Clinical Significance
Conservation
PhyloP100: 3.22
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
PM2
?
Very rare variant in population databases, with high coverage;
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.24).
Transcripts
RefSeq
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Ensembl
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Frequencies
GnomAD3 genomes ? AF: 0.0000328 AC: 5AN: 152244Hom.: 0 Cov.: 33
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GnomAD4 exome AF: 0.0000196 AC: 10AN: 509718Hom.: 0 Cov.: 5 AF XY: 0.0000221 AC XY: 6AN XY: 271778
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GnomAD4 genome ? AF: 0.0000394 AC: 6AN: 152362Hom.: 0 Cov.: 33 AF XY: 0.0000268 AC XY: 2AN XY: 74500
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ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Hereditary cancer-predisposing syndrome Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jun 26, 2020 | The c.-196G>A variant is located in the 5' untranslated region (5’ UTR) of the MSH2 gene. This variant results from a G to A substitution 196 bases upstream from the first translated codon. A variant at a nearby position (c.-190G>A, also known as c.-181G>A) was detected in an individual with MSI-H colorectal cancer diagnosed before age 40; a luciferase assay showed that promoter activity was decreased by 77% compared to wildtype (Shin KH et al. Cancer Res. 2002 Jan;62:38-42). This nucleotide position is highly conserved in available vertebrate species. Since supporting evidence is limited at this time, the clinical significance of this alteration remains unclear. - |
Computational scores
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Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at