GeneBe

rs755407736

Variant names:

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 2P and 2B. PM2BP4_Moderate

The NM_001085480.3(FAM162B):​c.58G>C​(p.Gly20Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 15/22 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. G20S) has been classified as Uncertain significance.

Frequency

Genomes: not found (cov: 32)
Exomes 𝑓: 0.0 ( 0 hom. )
Failed GnomAD Quality Control

Consequence

FAM162B
NM_001085480.3 missense

Scores

2
16

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: -0.154

Publications

0 publications found
Variant links:
Genes affected
FAM162B (HGNC:21549): (family with sequence similarity 162 member B) Predicted to be integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]

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ACMG classification

Classification was made for transcript

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.06806517).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001085480.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.
GeneTranscriptTagsHGVScHGVSpEffectExon RankProteinUniProt
FAM162B
NM_001085480.3
MANE Select
c.58G>Cp.Gly20Arg
missense
Exon 1 of 4NP_001078949.1Q5T6X4

Ensembl Transcripts

Sel.
GeneTranscriptTagsHGVScHGVSpEffectExon RankProteinUniProt
FAM162B
ENST00000368557.6
TSL:1 MANE Select
c.58G>Cp.Gly20Arg
missense
Exon 1 of 4ENSP00000357545.4Q5T6X4
FAM162B
ENST00000864732.1
c.58G>Cp.Gly20Arg
missense
Exon 1 of 4ENSP00000534793.1

Frequencies

GnomAD3 genomes
Cov.:
32
GnomAD4 exome
Data not reliable, filtered out with message: AC0
AF:
0.00
AC:
0
AN:
1243452
Hom.:
0
Cov.:
31
AF XY:
0.00
AC XY:
0
AN XY:
600544
African (AFR)
AF:
0.00
AC:
0
AN:
24340
American (AMR)
AF:
0.00
AC:
0
AN:
15084
Ashkenazi Jewish (ASJ)
AF:
0.00
AC:
0
AN:
17530
East Asian (EAS)
AF:
0.00
AC:
0
AN:
29810
South Asian (SAS)
AF:
0.00
AC:
0
AN:
56290
European-Finnish (FIN)
AF:
0.00
AC:
0
AN:
30738
Middle Eastern (MID)
AF:
0.00
AC:
0
AN:
3464
European-Non Finnish (NFE)
AF:
0.00
AC:
0
AN:
1014616
Other (OTH)
AF:
0.00
AC:
0
AN:
51580
GnomAD4 genome
Cov.:
32
Alfa
AF:
0.00
Hom.:
0
Bravo
AF:
0.0000113

ClinVar

ClinVar submissions
Significance:Uncertain significance
Revision:criteria provided, single submitter
View on ClinVar
Pathogenic
VUS
Benign
Condition
-
1
-
not specified (1)

Computational scores

Source: dbNSFP v4.9

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.15
BayesDel_addAF
Benign
-0.26
T
BayesDel_noAF
Benign
-0.61
CADD
Benign
7.9
DANN
Benign
0.96
DEOGEN2
Benign
0.0012
T
Eigen
Benign
-1.4
Eigen_PC
Benign
-1.5
FATHMM_MKL
Benign
0.049
N
LIST_S2
Benign
0.45
T
M_CAP
Benign
0.0049
T
MetaRNN
Benign
0.068
T
MetaSVM
Benign
-1.0
T
MutationAssessor
Benign
1.1
L
PhyloP100
-0.15
PrimateAI
Uncertain
0.71
T
PROVEAN
Benign
-0.050
N
REVEL
Benign
0.031
Sift
Benign
0.034
D
Sift4G
Uncertain
0.0080
D
Polyphen
0.24
B
Vest4
0.17
MutPred
0.48
Gain of methylation at G20 (P = 0.0151)
MVP
0.040
MPC
0.80
ClinPred
0.17
T
GERP RS
-2.4
PromoterAI
-0.027
Neutral
Varity_R
0.074
gMVP
0.30
Mutation Taster
=94/6
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: rs755407736; hg19: chr6-117086682; API