chr8-138138991-T-C
Position:
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_015912.4(FAM135B):āc.3896A>Gā(p.Lys1299Arg) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000137 in 1,456,176 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Genomes: not found (cov: 33)
Exomes š: 0.0000014 ( 0 hom. )
Consequence
FAM135B
NM_015912.4 missense
NM_015912.4 missense
Scores
5
5
9
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 8.02
Genes affected
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 2 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
FAM135B | NM_015912.4 | c.3896A>G | p.Lys1299Arg | missense_variant | 18/20 | ENST00000395297.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FAM135B | ENST00000395297.6 | c.3896A>G | p.Lys1299Arg | missense_variant | 18/20 | 5 | NM_015912.4 | P1 | |
FAM135B | ENST00000482951.6 | c.*3842A>G | 3_prime_UTR_variant, NMD_transcript_variant | 19/21 | 1 | ||||
FAM135B | ENST00000276737.10 | c.*366A>G | 3_prime_UTR_variant, NMD_transcript_variant | 18/20 | 5 |
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD3 genomes
Cov.:
33
GnomAD4 exome AF: 0.00000137 AC: 2AN: 1456176Hom.: 0 Cov.: 28 AF XY: 0.00000276 AC XY: 2AN XY: 724872
GnomAD4 exome
AF:
AC:
2
AN:
1456176
Hom.:
Cov.:
28
AF XY:
AC XY:
2
AN XY:
724872
Gnomad4 AFR exome
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GnomAD4 genome Cov.: 33
GnomAD4 genome
Cov.:
33
Bravo
AF:
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Pathogenic
DANN
Uncertain
DEOGEN2
Benign
T
Eigen
Pathogenic
Eigen_PC
Pathogenic
FATHMM_MKL
Pathogenic
D
LIST_S2
Uncertain
D
M_CAP
Benign
T
MetaRNN
Uncertain
T
MetaSVM
Benign
T
MutationAssessor
Benign
L
MutationTaster
Benign
D
PrimateAI
Pathogenic
D
PROVEAN
Uncertain
N
REVEL
Uncertain
Sift
Benign
T
Sift4G
Pathogenic
D
Polyphen
D
Vest4
MutPred
Loss of methylation at K1299 (P = 0.0189);
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