chr16-254571-T-C
Position:
Variant summary
Our verdict is Uncertain significance. Variant got 3 ACMG points: 3P and 0B. PM2PP3
The NM_032039.4(FAM234A):āc.158T>Cā(p.Phe53Ser) variant causes a missense change. The variant allele was found at a frequency of 0.00000205 in 1,461,832 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Genomes: not found (cov: 32)
Exomes š: 0.0000021 ( 0 hom. )
Consequence
FAM234A
NM_032039.4 missense
NM_032039.4 missense
Scores
7
7
3
Clinical Significance
Conservation
PhyloP100: 6.14
Genes affected
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 3 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
PP3
MetaRNN computational evidence supports a deleterious effect, 0.754
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
FAM234A | NM_032039.4 | c.158T>C | p.Phe53Ser | missense_variant | 3/13 | ENST00000399932.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FAM234A | ENST00000399932.8 | c.158T>C | p.Phe53Ser | missense_variant | 3/13 | 1 | NM_032039.4 | P1 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 genomes
Cov.:
32
GnomAD4 exome AF: 0.00000205 AC: 3AN: 1461832Hom.: 0 Cov.: 33 AF XY: 0.00000275 AC XY: 2AN XY: 727204
GnomAD4 exome
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3
AN:
1461832
Hom.:
Cov.:
33
AF XY:
AC XY:
2
AN XY:
727204
Gnomad4 AFR exome
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GnomAD4 genome Cov.: 32
GnomAD4 genome
Cov.:
32
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 | Nov 21, 2023 | The c.158T>C (p.F53S) alteration is located in exon 3 (coding exon 1) of the FAM234A gene. This alteration results from a T to C substitution at nucleotide position 158, causing the phenylalanine (F) at amino acid position 53 to be replaced by a serine (S). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Pathogenic
BayesDel_addAF
Pathogenic
D
BayesDel_noAF
Pathogenic
CADD
Uncertain
DANN
Uncertain
DEOGEN2
Benign
T;.;.;.;.;.;.;.;T;.;.;.
Eigen
Uncertain
Eigen_PC
Uncertain
FATHMM_MKL
Pathogenic
D
M_CAP
Benign
D
MetaRNN
Pathogenic
D;D;D;D;D;D;D;D;D;D;D;D
MetaSVM
Uncertain
T
MutationTaster
Benign
D;D;D;D;D
PrimateAI
Uncertain
T
PROVEAN
Pathogenic
D;D;D;D;D;D;D;D;D;D;D;.
REVEL
Uncertain
Sift
Uncertain
D;D;D;D;D;D;D;D;D;D;D;.
Sift4G
Pathogenic
D;D;D;D;D;D;D;D;D;D;D;D
Polyphen
D;D;.;.;.;.;.;.;D;.;.;.
Vest4
MutPred
Gain of catalytic residue at F53 (P = 0.0123);Gain of catalytic residue at F53 (P = 0.0123);Gain of catalytic residue at F53 (P = 0.0123);Gain of catalytic residue at F53 (P = 0.0123);Gain of catalytic residue at F53 (P = 0.0123);Gain of catalytic residue at F53 (P = 0.0123);Gain of catalytic residue at F53 (P = 0.0123);Gain of catalytic residue at F53 (P = 0.0123);Gain of catalytic residue at F53 (P = 0.0123);Gain of catalytic residue at F53 (P = 0.0123);Gain of catalytic residue at F53 (P = 0.0123);Gain of catalytic residue at F53 (P = 0.0123);
MVP
MPC
ClinPred
D
GERP RS
Varity_R
gMVP
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at