NM_001377989.1:c.232G>A

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 0P and 2B. BP4_Moderate

The NM_001377989.1(FAM110B):​c.232G>A​(p.Ala78Thr) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000112 in 1,613,228 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/22 in silico tools predict 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. A78S) has been classified as Uncertain significance.

Frequency

Genomes: 𝑓 0.000026 ( 0 hom., cov: 33)
Exomes 𝑓: 0.0000096 ( 0 hom. )

Consequence

FAM110B
NM_001377989.1 missense

Scores

5
14

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 7.29

Publications

1 publications found
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 was made for transcript

Our verdict: Likely_benign. The variant received -2 ACMG points.

BP4
Computational evidence support a benign effect (MetaRNN=0.14071229).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
FAM110BNM_001377989.1 linkc.232G>A p.Ala78Thr 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.232G>A p.Ala78Thr missense_variant Exon 4 of 4 2 NM_001377989.1 ENSP00000509301.1 Q8TC76
FAM110BENST00000361488.7 linkc.232G>A p.Ala78Thr missense_variant Exon 5 of 5 2 ENSP00000355204.3 Q8TC76
FAM110BENST00000520369.5 linkn.427-51369G>A intron_variant Intron 3 of 4 4
FAM110BENST00000523486.5 linkn.226-42856G>A intron_variant Intron 2 of 3 4

Frequencies

GnomAD3 genomes
AF:
0.0000263
AC:
4
AN:
152076
Hom.:
0
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.00
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.000262
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.00
Gnomad OTH
AF:
0.00
GnomAD2 exomes
AF:
0.0000482
AC:
12
AN:
248992
AF XY:
0.0000297
show subpopulations
Gnomad AFR exome
AF:
0.00
Gnomad AMR exome
AF:
0.000319
Gnomad ASJ exome
AF:
0.00
Gnomad EAS 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:
0.00000958
AC:
14
AN:
1461152
Hom.:
0
Cov.:
31
AF XY:
0.00000963
AC XY:
7
AN XY:
726852
show subpopulations
African (AFR)
AF:
0.00
AC:
0
AN:
33468
American (AMR)
AF:
0.000246
AC:
11
AN:
44686
Ashkenazi Jewish (ASJ)
AF:
0.00
AC:
0
AN:
26092
East Asian (EAS)
AF:
0.00
AC:
0
AN:
39682
South Asian (SAS)
AF:
0.0000232
AC:
2
AN:
86200
European-Finnish (FIN)
AF:
0.00
AC:
0
AN:
53270
Middle Eastern (MID)
AF:
0.00
AC:
0
AN:
5764
European-Non Finnish (NFE)
AF:
9.00e-7
AC:
1
AN:
1111630
Other (OTH)
AF:
0.00
AC:
0
AN:
60360
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.464
Heterozygous variant carriers
0
1
3
4
6
7
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Exome Het
Variant carriers
0
2
4
6
8
10
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
GnomAD4 genome
AF:
0.0000263
AC:
4
AN:
152076
Hom.:
0
Cov.:
33
AF XY:
0.0000404
AC XY:
3
AN XY:
74272
show subpopulations
African (AFR)
AF:
0.00
AC:
0
AN:
41404
American (AMR)
AF:
0.000262
AC:
4
AN:
15284
Ashkenazi Jewish (ASJ)
AF:
0.00
AC:
0
AN:
3468
East Asian (EAS)
AF:
0.00
AC:
0
AN:
5156
South Asian (SAS)
AF:
0.00
AC:
0
AN:
4826
European-Finnish (FIN)
AF:
0.00
AC:
0
AN:
10608
Middle Eastern (MID)
AF:
0.00
AC:
0
AN:
316
European-Non Finnish (NFE)
AF:
0.00
AC:
0
AN:
68016
Other (OTH)
AF:
0.00
AC:
0
AN:
2086
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.500
Heterozygous variant carriers
0
1
1
2
2
3
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Alfa
AF:
0.00
Hom.:
0
Bravo
AF:
0.0000189
ExAC
AF:
0.0000330
AC:
4

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.089
BayesDel_addAF
Benign
-0.42
T
BayesDel_noAF
Benign
-0.53
CADD
Benign
23
DANN
Uncertain
1.0
DEOGEN2
Benign
0.043
T
Eigen
Uncertain
0.27
Eigen_PC
Uncertain
0.30
FATHMM_MKL
Uncertain
0.87
D
LIST_S2
Benign
0.86
D
M_CAP
Benign
0.038
D
MetaRNN
Benign
0.14
T
MetaSVM
Benign
-1.0
T
MutationAssessor
Benign
1.5
L
PhyloP100
7.3
PrimateAI
Uncertain
0.74
T
PROVEAN
Benign
-0.73
N
REVEL
Benign
0.11
Sift
Benign
0.43
T
Sift4G
Benign
0.72
T
Polyphen
0.93
P
Vest4
0.26
MutPred
0.19
Gain of glycosylation at A78 (P = 0.0235);
MVP
0.44
MPC
0.88
ClinPred
0.27
T
GERP RS
3.7
Varity_R
0.082
gMVP
0.39
Mutation Taster
=70/30
polymorphism

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

Other links and lift over

dbSNP: rs761969859; hg19: chr8-59059021; COSMIC: COSV64068652; COSMIC: COSV64068652; API