rs1257642100
Positions:
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The variant allele was found at a frequency of 0.0000161 in 373,648 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 Benign (★).
Frequency
Genomes: 𝑓 0.000026 ( 0 hom., cov: 33)
Exomes 𝑓: 0.0000090 ( 0 hom. )
Consequence
Unknown
Scores
2
Clinical Significance
Conservation
PhyloP100: -2.71
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
PM2
?
Very rare variant in population databases, with high coverage;
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.82).
BP6
?
Variant 5-112707389-A-C is Benign according to our data. Variant chr5-112707389-A-C is described in ClinVar as [Benign]. Clinvar id is 469885.Status of the report is criteria_provided_single_submitter, 1 stars.
Transcripts
RefSeq
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Ensembl
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Frequencies
GnomAD3 genomes ? AF: 0.0000263 AC: 4AN: 152292Hom.: 0 Cov.: 33
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GnomAD4 exome AF: 0.00000904 AC: 2AN: 221356Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 113532
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GnomAD4 genome ? AF: 0.0000263 AC: 4AN: 152292Hom.: 0 Cov.: 33 AF XY: 0.0000269 AC XY: 2AN XY: 74412
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Familial adenomatous polyposis 1 Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 29, 2024 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at