rs1248082128

Variant summary

Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4

The NM_001377989.1(FAM110B):​c.251C>G​(p.Pro84Arg) variant causes a missense change. The variant allele was found at a frequency of 0.000000684 in 1,461,322 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 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. P84L) has been classified as Uncertain significance.

Frequency

Genomes: not found (cov: 33)
Exomes š‘“: 6.8e-7 ( 0 hom. )

Consequence

FAM110B
NM_001377989.1 missense

Scores

1
7
11

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 4.55
Variant links:
Genes affected
FAM110B (HGNC:28587): (family with sequence similarity 110 member B) Located in cytosol and mitochondrion. [provided by Alliance of Genome Resources, Apr 2022]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 1 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.39270312).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
FAM110BNM_001377989.1 linkc.251C>G p.Pro84Arg missense_variant Exon 4 of 4 ENST00000519262.6 NP_001364918.1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
FAM110BENST00000519262.6 linkc.251C>G p.Pro84Arg missense_variant Exon 4 of 4 2 NM_001377989.1 ENSP00000509301.1 Q8TC76
FAM110BENST00000361488.7 linkc.251C>G p.Pro84Arg missense_variant Exon 5 of 5 2 ENSP00000355204.3 Q8TC76
FAM110BENST00000520369.5 linkn.427-51350C>G intron_variant Intron 3 of 4 4
FAM110BENST00000523486.5 linkn.226-42837C>G intron_variant Intron 2 of 3 4

Frequencies

GnomAD3 genomes
Cov.:
33
GnomAD3 exomes
AF:
0.00000402
AC:
1
AN:
248606
Hom.:
0
AF XY:
0.00
AC XY:
0
AN XY:
134686
show subpopulations
Gnomad AFR exome
AF:
0.00
Gnomad AMR exome
AF:
0.0000290
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.00
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.00
Gnomad OTH exome
AF:
0.00
GnomAD4 exome
AF:
6.84e-7
AC:
1
AN:
1461322
Hom.:
0
Cov.:
31
AF XY:
0.00
AC XY:
0
AN XY:
726954
show subpopulations
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.0000224
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.00
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
Cov.:
33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.29
BayesDel_addAF
Benign
-0.15
T
BayesDel_noAF
Benign
-0.36
CADD
Benign
23
DANN
Uncertain
1.0
DEOGEN2
Uncertain
0.58
D
Eigen
Uncertain
0.46
Eigen_PC
Uncertain
0.48
FATHMM_MKL
Uncertain
0.86
D
LIST_S2
Uncertain
0.88
D
M_CAP
Benign
0.042
D
MetaRNN
Benign
0.39
T
MetaSVM
Benign
-0.93
T
MutationAssessor
Uncertain
2.4
M
PrimateAI
Pathogenic
0.80
T
PROVEAN
Benign
-1.4
N
REVEL
Benign
0.11
Sift
Benign
0.073
T
Sift4G
Benign
0.13
T
Polyphen
0.99
D
Vest4
0.34
MutPred
0.27
Gain of MoRF binding (P = 0.0011);
MVP
0.45
MPC
1.7
ClinPred
0.79
D
GERP RS
5.4
Varity_R
0.15
gMVP
0.58

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs1248082128; hg19: chr8-59059040; API