chr14-73942608-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_152445.3(FAM161B):c.1033C>T(p.Arg345Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000768 in 1,614,074 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 0.00020 ( 0 hom., cov: 32)
Exomes 𝑓: 0.000064 ( 0 hom. )
Consequence
FAM161B
NM_152445.3 missense
NM_152445.3 missense
Scores
3
5
9
Clinical Significance
Conservation
PhyloP100: 2.73
Genes affected
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ACMG classification
Classification made for transcript
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 (MetaRNN=0.16816899).
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
FAM161B | NM_152445.3 | c.1033C>T | p.Arg345Cys | missense_variant | 4/9 | ENST00000286544.5 | |
FAM161B | XM_011536475.3 | c.1033C>T | p.Arg345Cys | missense_variant | 4/10 | ||
FAM161B | XR_007063990.1 | n.1101C>T | non_coding_transcript_exon_variant | 4/11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FAM161B | ENST00000286544.5 | c.1033C>T | p.Arg345Cys | missense_variant | 4/9 | 1 | NM_152445.3 | P1 | |
FAM161B | ENST00000651776.1 | c.1222C>T | p.Arg408Cys | missense_variant | 4/9 |
Frequencies
GnomAD3 genomes ? AF: 0.000204 AC: 31AN: 152184Hom.: 0 Cov.: 32
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?
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GnomAD3 exomes AF: 0.0000876 AC: 22AN: 251170Hom.: 0 AF XY: 0.0000663 AC XY: 9AN XY: 135782
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GnomAD4 exome AF: 0.0000636 AC: 93AN: 1461890Hom.: 0 Cov.: 32 AF XY: 0.0000619 AC XY: 45AN XY: 727246
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GnomAD4 genome ? AF: 0.000204 AC: 31AN: 152184Hom.: 0 Cov.: 32 AF XY: 0.000161 AC XY: 12AN XY: 74354
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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 | Mar 28, 2023 | The c.1222C>T (p.R408C) alteration is located in exon 4 (coding exon 4) of the FAM161B gene. This alteration results from a C to T substitution at nucleotide position 1222, causing the arginine (R) at amino acid position 408 to be replaced by a cysteine (C). 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
Pathogenic
Dann
Pathogenic
Eigen
Pathogenic
Eigen_PC
Pathogenic
FATHMM_MKL
Uncertain
D
LIST_S2
Uncertain
D
M_CAP
Benign
D
MetaRNN
Benign
T
MetaSVM
Benign
T
MutationTaster
Benign
D;D
PrimateAI
Benign
T
PROVEAN
Uncertain
D
REVEL
Benign
Sift
Uncertain
D
Sift4G
Uncertain
D
Vest4
MVP
MPC
ClinPred
D
GERP RS
Splicing
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Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at