rs1210344444

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong

The NM_001137610.3(FAM86B2):​c.651C>G​(p.Asp217Glu) 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: 19)
Exomes š‘“: 8.8e-7 ( 0 hom. )
Failed GnomAD Quality Control

Consequence

FAM86B2
NM_001137610.3 missense

Scores

1
18

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.250
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 -4 ACMG points.

BP4
Computational evidence support a benign effect (MetaRNN=0.044837862).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
FAM86B2NM_001137610.3 linkc.651C>G p.Asp217Glu missense_variant Exon 6 of 8 ENST00000262365.9 NP_001131082.1 P0C5J1
FAM86B2NR_148876.2 linkn.431+257C>G intron_variant Intron 4 of 5
FAM86B2NR_148877.2 linkn.350+257C>G intron_variant Intron 3 of 4
FAM86B2NR_148878.2 linkn.631+257C>G intron_variant Intron 5 of 6

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
FAM86B2ENST00000262365.9 linkc.651C>G p.Asp217Glu missense_variant Exon 6 of 8 5 NM_001137610.3 ENSP00000262365.4 P0C5J1

Frequencies

GnomAD3 genomes
Cov.:
19
GnomAD3 exomes
AF:
0.00000838
AC:
1
AN:
119302
Hom.:
0
AF XY:
0.0000157
AC XY:
1
AN XY:
63532
show subpopulations
Gnomad AFR exome
AF:
0.00
Gnomad AMR exome
AF:
0.00
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:
0.0000196
Gnomad OTH exome
AF:
0.00
GnomAD4 exome
Data not reliable, filtered out with message: AS_VQSR
AF:
8.75e-7
AC:
1
AN:
1142590
Hom.:
0
Cov.:
28
AF XY:
0.00000176
AC XY:
1
AN XY:
569468
show subpopulations
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.00
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.00000115
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
Cov.:
19

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.11
BayesDel_addAF
Benign
-0.45
T
BayesDel_noAF
Benign
-0.89
CADD
Benign
0.67
DANN
Benign
0.91
DEOGEN2
Benign
0.0015
T;.
Eigen
Benign
-1.2
Eigen_PC
Benign
-1.3
FATHMM_MKL
Benign
0.0029
N
LIST_S2
Benign
0.35
T;T
M_CAP
Benign
0.00085
T
MetaRNN
Benign
0.045
T;T
MetaSVM
Benign
-0.91
T
MutationAssessor
Benign
-0.17
N;.
PrimateAI
Uncertain
0.53
T
PROVEAN
Benign
-0.69
N;N
REVEL
Benign
0.010
Sift
Benign
0.51
T;T
Sift4G
Benign
0.39
T;T
Polyphen
0.0
B;.
Vest4
0.061
MutPred
0.39
Gain of disorder (P = 0.1738);.;
MVP
0.043
MPC
1.9
ClinPred
0.018
T
GERP RS
0.17
Varity_R
0.033
gMVP
0.21

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: rs1210344444; hg19: chr8-12286233; API