10-122336546-A-G

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong

The NM_144587.5(BTBD16):​c.1316A>G​(p.His439Arg) 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. 15/21 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. H439P) has been classified as Likely benign.

Frequency

Genomes: not found (cov: 33)

Consequence

BTBD16
NM_144587.5 missense

Scores

2
17

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0910
Variant links:
Genes affected
BTBD16 (HGNC:26340): (BTB domain containing 16) This gene encodes a protein that contains a BTB/POZ domain. This domain mediates protein-protein interactions. A mutation in this gene may be associated with bipolar disorder. [provided by RefSeq, Sep 2016]

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ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -2 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.04993248).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
BTBD16NM_144587.5 linkuse as main transcriptc.1316A>G p.His439Arg missense_variant 15/16 ENST00000260723.6 NP_653188.2

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
BTBD16ENST00000260723.6 linkuse as main transcriptc.1316A>G p.His439Arg missense_variant 15/162 NM_144587.5 ENSP00000260723 P1Q32M84-1
BTBD16ENST00000495370.2 linkuse as main transcriptn.522A>G non_coding_transcript_exon_variant 4/43

Frequencies

GnomAD3 genomes
Cov.:
33
GnomAD4 exome
Cov.:
35
GnomAD4 genome
Cov.:
33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.068
BayesDel_addAF
Benign
-0.38
T
BayesDel_noAF
Benign
-0.79
CADD
Benign
6.0
DANN
Benign
0.77
DEOGEN2
Benign
0.0027
T
Eigen
Benign
-1.3
Eigen_PC
Benign
-1.3
FATHMM_MKL
Benign
0.021
N
LIST_S2
Benign
0.34
T
M_CAP
Benign
0.0035
T
MetaRNN
Benign
0.050
T
MetaSVM
Benign
-1.0
T
MutationAssessor
Benign
0.0
N
MutationTaster
Benign
1.0
P;P
PrimateAI
Benign
0.28
T
PROVEAN
Benign
-0.31
N
REVEL
Benign
0.024
Sift
Uncertain
0.024
D
Sift4G
Uncertain
0.023
D
Polyphen
0.0
B
Vest4
0.043
MutPred
0.46
Gain of MoRF binding (P = 0.0084);
MVP
0.15
MPC
0.17
ClinPred
0.10
T
GERP RS
1.4
Varity_R
0.038
gMVP
0.15

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: rs1048347; hg19: chr10-124096061; API