chr12-13068306-A-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 0P and 2B. BP6_Moderate
The NM_020853.2(FAM234B):c.1145A>T(p.Asp382Val) variant causes a missense, splice region change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000457 in 1,614,118 control chromosomes in the GnomAD database, including 5 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.00037 ( 0 hom., cov: 33)
Exomes 𝑓: 0.00047 ( 5 hom. )
Consequence
FAM234B
NM_020853.2 missense, splice_region
NM_020853.2 missense, splice_region
Scores
6
11
Clinical Significance
Conservation
PhyloP100: 3.26
Genes affected
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -2 ACMG points.
BP6
?
Variant 12-13068306-A-T is Benign according to our data. Variant chr12-13068306-A-T is described in ClinVar as [Likely_benign]. Clinvar id is 3035768.Status of the report is criteria_provided_single_submitter, 1 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
FAM234B | NM_020853.2 | c.1145A>T | p.Asp382Val | missense_variant, splice_region_variant | 8/13 | ENST00000197268.13 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FAM234B | ENST00000197268.13 | c.1145A>T | p.Asp382Val | missense_variant, splice_region_variant | 8/13 | 1 | NM_020853.2 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000375 AC: 57AN: 152202Hom.: 0 Cov.: 33
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GnomAD3 exomes AF: 0.000777 AC: 195AN: 251092Hom.: 1 AF XY: 0.000884 AC XY: 120AN XY: 135682
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GnomAD4 exome AF: 0.000465 AC: 680AN: 1461798Hom.: 5 Cov.: 31 AF XY: 0.000594 AC XY: 432AN XY: 727202
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GnomAD4 genome ? AF: 0.000374 AC: 57AN: 152320Hom.: 0 Cov.: 33 AF XY: 0.000416 AC XY: 31AN XY: 74486
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
FAM234B-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Aug 05, 2019 | This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
Cadd
Pathogenic
Dann
Uncertain
DEOGEN2
Benign
T;.
Eigen
Uncertain
Eigen_PC
Uncertain
FATHMM_MKL
Uncertain
D
M_CAP
Benign
D
MetaRNN
Benign
T;T
MetaSVM
Benign
T
MutationTaster
Benign
D
PrimateAI
Uncertain
T
PROVEAN
Benign
N;N
REVEL
Benign
Sift
Uncertain
D;D
Sift4G
Benign
T;D
Polyphen
D;.
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
DS_AG_spliceai
Position offset: 20
Find out detailed SpliceAI scores and Pangolin per-transcript scores at