GeneBe

rs777802537

Variant names:

Variant summary

Our verdict is Uncertain significance. The variant received 2 ACMG points: 2P and 0B. PM2

The NM_173611.4(FAM98B):​c.316C>A​(p.Arg106Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R106C) has been classified as Uncertain significance.

Frequency

Genomes: not found (cov: 33)
Exomes 𝑓: 0.0 ( 0 hom. )
Failed GnomAD Quality Control

Consequence

FAM98B
NM_173611.4 missense

Scores

1
9
8

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 3.07

Publications

6 publications found
Variant links:
Genes affected
FAM98B (HGNC:26773): (family with sequence similarity 98 member B) Enables identical protein binding activity and protein methyltransferase activity. Involved in positive regulation of cell population proliferation; positive regulation of gene expression; and protein methylation. Located in cytoplasm and nucleoplasm. Part of tRNA-splicing ligase complex. [provided by Alliance of Genome Resources, Apr 2022]

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Uncertain_significance. The variant received 2 ACMG points.

PM2
Very rare variant in population databases, with high coverage;

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_173611.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.
GeneTranscriptTagsHGVScHGVSpEffectExon RankProteinUniProt
FAM98B
NM_173611.4
MANE Select
c.316C>Ap.Arg106Ser
missense
Exon 3 of 8NP_775882.2Q52LJ0-2

Ensembl Transcripts

Sel.
GeneTranscriptTagsHGVScHGVSpEffectExon RankProteinUniProt
FAM98B
ENST00000397609.6
TSL:5 MANE Select
c.316C>Ap.Arg106Ser
missense
Exon 3 of 8ENSP00000380734.2Q52LJ0-2
FAM98B
ENST00000491535.5
TSL:1
c.316C>Ap.Arg106Ser
missense
Exon 3 of 7ENSP00000453166.1Q52LJ0-1
FAM98B
ENST00000559431.1
TSL:5
c.22C>Ap.Arg8Ser
missense
Exon 1 of 4ENSP00000453926.1H0YNA1

Frequencies

GnomAD3 genomes
Cov.:
33
GnomAD4 exome
Data not reliable, filtered out with message: AC0
AF:
0.00
AC:
0
AN:
1449378
Hom.:
0
Cov.:
30
AF XY:
0.00
AC XY:
0
AN XY:
720632
African (AFR)
AF:
0.00
AC:
0
AN:
32940
American (AMR)
AF:
0.00
AC:
0
AN:
42634
Ashkenazi Jewish (ASJ)
AF:
0.00
AC:
0
AN:
25784
East Asian (EAS)
AF:
0.00
AC:
0
AN:
39304
South Asian (SAS)
AF:
0.00
AC:
0
AN:
82950
European-Finnish (FIN)
AF:
0.00
AC:
0
AN:
53050
Middle Eastern (MID)
AF:
0.00
AC:
0
AN:
5718
European-Non Finnish (NFE)
AF:
0.00
AC:
0
AN:
1107158
Other (OTH)
AF:
0.00
AC:
0
AN:
59840
GnomAD4 genome
Cov.:
33
TwinsUK
AF:
0.000270
AC:
1
ALSPAC
AF:
0.00
AC:
0

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Pathogenic
0.98
BayesDel_addAF
Benign
-0.043
T
BayesDel_noAF
Benign
-0.30
CADD
Uncertain
24
DANN
Uncertain
1.0
DEOGEN2
Benign
0.22
T
Eigen
Uncertain
0.25
Eigen_PC
Uncertain
0.30
FATHMM_MKL
Benign
0.58
D
LIST_S2
Uncertain
0.87
D
M_CAP
Benign
0.0095
T
MetaRNN
Uncertain
0.61
D
MetaSVM
Benign
-0.89
T
MutationAssessor
Uncertain
2.2
M
PhyloP100
3.1
PrimateAI
Uncertain
0.54
T
PROVEAN
Uncertain
-3.9
D
REVEL
Benign
0.18
Sift
Uncertain
0.0060
D
Sift4G
Benign
0.064
T
Polyphen
0.81
P
Vest4
0.34
MutPred
0.72
Gain of ubiquitination at K109 (P = 0.0444)
MVP
0.65
MPC
0.59
ClinPred
0.96
D
GERP RS
4.8
PromoterAI
0.017
Neutral
Varity_R
0.42
gMVP
0.69

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.030
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

Other links and lift over

dbSNP: rs777802537; hg19: chr15-38757568; API