rs201696967

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 0P and 2B. BP4_Moderate

The NM_001137610.3(FAM86B2):​c.838G>T​(p.Val280Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: not found (cov: 13)
Exomes 𝑓: 0.0000010 ( 0 hom. )
Failed GnomAD Quality Control

Consequence

FAM86B2
NM_001137610.3 missense

Scores

2
17

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.761
Variant links:
Genes affected
FAM86B2 (HGNC:32222): (family with sequence similarity 86 member B2) Predicted to enable methyltransferase activity. Predicted to be involved in methylation. Part of protein-containing complex. [provided by Alliance of Genome Resources, Apr 2022]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -2 ACMG points.

BP4
Computational evidence support a benign effect (MetaRNN=0.13634041).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
FAM86B2NM_001137610.3 linkc.838G>T p.Val280Leu missense_variant Exon 7 of 8 ENST00000262365.9 NP_001131082.1 P0C5J1
FAM86B2NR_148876.2 linkn.527G>T non_coding_transcript_exon_variant Exon 5 of 6
FAM86B2NR_148877.2 linkn.446G>T non_coding_transcript_exon_variant Exon 4 of 5
FAM86B2NR_148878.2 linkn.727G>T non_coding_transcript_exon_variant Exon 6 of 7

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
FAM86B2ENST00000262365.9 linkc.838G>T p.Val280Leu missense_variant Exon 7 of 8 5 NM_001137610.3 ENSP00000262365.4 P0C5J1

Frequencies

GnomAD3 genomes
Cov.:
13
GnomAD4 exome
Data not reliable, filtered out with message: AS_VQSR
AF:
0.00000100
AC:
1
AN:
1000108
Hom.:
0
Cov.:
33
AF XY:
0.00
AC XY:
0
AN XY:
498988
show subpopulations
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.00
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.0000329
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.:
13
ExAC
AF:
0.0000115
AC:
1

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.14
BayesDel_addAF
Benign
-0.28
T
BayesDel_noAF
Benign
-0.65
CADD
Benign
2.6
DANN
Benign
0.91
DEOGEN2
Benign
0.0095
T;T;.
Eigen
Benign
-1.5
Eigen_PC
Benign
-1.6
FATHMM_MKL
Benign
0.045
N
LIST_S2
Uncertain
0.94
D;D;D
M_CAP
Benign
0.0072
T
MetaRNN
Benign
0.14
T;T;T
MetaSVM
Benign
-1.1
T
MutationAssessor
Benign
0.94
L;.;.
PrimateAI
Uncertain
0.69
T
PROVEAN
Benign
-1.7
N;.;N
REVEL
Benign
0.026
Sift
Benign
0.046
D;.;T
Sift4G
Benign
0.30
T;D;T
Polyphen
0.023
B;.;.
Vest4
0.31
MutPred
0.60
Gain of sheet (P = 0.0221);.;.;
MVP
0.082
MPC
1.7
ClinPred
0.044
T
GERP RS
-0.54
Varity_R
0.12
gMVP
0.54

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: rs201696967; hg19: chr8-12285220; API