8-12186519-C-T
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Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 0P and 2B. BP4_Moderate
The NM_001083537.4(FAM86B1):c.473G>A(p.Arg158Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: 𝑓 0.000059 ( 0 hom., cov: 25)
Exomes 𝑓: 0.000040 ( 0 hom. )
Failed GnomAD Quality Control
Consequence
FAM86B1
NM_001083537.4 missense
NM_001083537.4 missense
Scores
18
Clinical Significance
Conservation
PhyloP100: -1.21
Genes affected
FAM86B1 (HGNC:28268): (family with sequence similarity 86 member B1) Predicted to enable methyltransferase activity. Predicted to be involved in methylation. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -2 ACMG points.
BP4
Computational evidence support a benign effect (MetaRNN=0.08374104).
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
FAM86B1 | NM_001083537.4 | c.473G>A | p.Arg158Gln | missense_variant | 5/7 | ENST00000448228.7 | |
FAM85A | NR_146925.1 | n.784C>T | non_coding_transcript_exon_variant | 1/4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FAM86B1 | ENST00000448228.7 | c.473G>A | p.Arg158Gln | missense_variant | 5/7 | 5 | NM_001083537.4 |
Frequencies
GnomAD3 genomes AF: 0.00 AC: 9AN: 151898Hom.: 0 Cov.: 25 FAILED QC
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GnomAD3 exomes AF: 0.0000280 AC: 7AN: 249570Hom.: 0 AF XY: 0.0000296 AC XY: 4AN XY: 135334
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GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.0000404 AC: 59AN: 1459272Hom.: 0 Cov.: 33 AF XY: 0.0000386 AC XY: 28AN XY: 725920
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GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR AF: 0.0000592 AC: 9AN: 152014Hom.: 0 Cov.: 25 AF XY: 0.0000807 AC XY: 6AN XY: 74350
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ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | May 04, 2023 | The c.473G>A (p.R158Q) alteration is located in exon 5 (coding exon 5) of the FAM86B1 gene. This alteration results from a G to A substitution at nucleotide position 473, causing the arginine (R) at amino acid position 158 to be replaced by a glutamine (Q). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
DEOGEN2
Benign
T;.
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Benign
N
LIST_S2
Benign
T;T
M_CAP
Benign
T
MetaRNN
Benign
T;T
MetaSVM
Benign
T
MutationAssessor
Benign
N;.
MutationTaster
Benign
N;N;N;N;N;N
PROVEAN
Benign
N;N
REVEL
Benign
Sift
Benign
T;T
Sift4G
Benign
T;T
Polyphen
B;B
Vest4
MVP
MPC
ClinPred
T
GERP RS
Varity_R
gMVP
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