rs2452658
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong
The NR_040092.1(FAM86B2-DT):n.1337-14285A>G variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.51 ( 2040 hom., cov: 83)
Failed GnomAD Quality Control
Consequence
FAM86B2-DT
NR_040092.1 intron, non_coding_transcript
NR_040092.1 intron, non_coding_transcript
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.0690
Genes affected
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -4 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.91).
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
FAM86B2-DT | NR_040092.1 | n.1337-14285A>G | intron_variant, non_coding_transcript_variant | ||||
LOC729732 | NR_047662.2 | n.1996-12536T>C | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ENST00000641618.1 | n.587+29227T>C | intron_variant, non_coding_transcript_variant | |||||||
ENST00000635775.1 | n.1973-12536T>C | intron_variant, non_coding_transcript_variant | 2 | ||||||
ENST00000641839.1 | n.684-40344T>C | intron_variant, non_coding_transcript_variant | |||||||
ENST00000711527.1 | n.679+49557T>C | intron_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomes ? AF: 0.00 AC: 74213AN: 145962Hom.: 2037 Cov.: 83 FAILED QC
GnomAD3 genomes
?
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AC:
74213
AN:
145962
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Cov.:
83
FAILED QC
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? Data not reliable, filtered out with message: InbreedingCoeff AF: 0.508 AC: 74266AN: 146060Hom.: 2040 Cov.: 83 AF XY: 0.510 AC XY: 36420AN XY: 71410
GnomAD4 genome
?
Data not reliable, filtered out with message: InbreedingCoeff
AF:
AC:
74266
AN:
146060
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Cov.:
83
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36420
AN XY:
71410
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ClinVar
Not reported inComputational 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