9-92718752-G-C

Variant summary

Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4

The NM_001003800.2(BICD2):ā€‹c.1893C>Gā€‹(p.Ile631Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000137 in 1,461,776 control chromosomes in the GnomAD database, with no homozygous occurrence. 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: 33)
Exomes š‘“: 0.0000014 ( 0 hom. )

Consequence

BICD2
NM_001003800.2 missense

Scores

1
18

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.10
Variant links:
Genes affected
BICD2 (HGNC:17208): (BICD cargo adaptor 2) This gene is one of two human homologs of Drosophila bicaudal-D and a member of the Bicoid family. It has been implicated in dynein-mediated, minus end-directed motility along microtubules. It has also been reported to be a phosphorylation target of NIMA related kinase 8. Two alternative splice variants have been described. [provided by RefSeq, Jul 2008]

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ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 1 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.28422356).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
BICD2NM_001003800.2 linkc.1893C>G p.Ile631Met missense_variant 5/7 ENST00000356884.11 NP_001003800.1 Q8TD16-2Q96FU2
BICD2NM_015250.4 linkc.1893C>G p.Ile631Met missense_variant 5/8 NP_056065.1 Q8TD16-1Q96FU2
BICD2XM_017014551.2 linkc.1974C>G p.Ile658Met missense_variant 5/8 XP_016870040.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
BICD2ENST00000356884.11 linkc.1893C>G p.Ile631Met missense_variant 5/71 NM_001003800.2 ENSP00000349351.6 Q8TD16-2
BICD2ENST00000375512.3 linkc.1893C>G p.Ile631Met missense_variant 5/81 ENSP00000364662.3 Q8TD16-1

Frequencies

GnomAD3 genomes
Cov.:
33
GnomAD4 exome
AF:
0.00000137
AC:
2
AN:
1461776
Hom.:
0
Cov.:
32
AF XY:
0.00000138
AC XY:
1
AN XY:
727194
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:
0.00000180
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
Cov.:
33
TwinsUK
AF:
0.00
AC:
0
ALSPAC
AF:
0.000259
AC:
1

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.32
BayesDel_addAF
Benign
-0.24
T
BayesDel_noAF
Benign
-0.58
CADD
Benign
5.4
DANN
Benign
0.97
DEOGEN2
Benign
0.27
.;T
Eigen
Benign
-0.95
Eigen_PC
Benign
-1.1
FATHMM_MKL
Benign
0.090
N
LIST_S2
Benign
0.84
T;T
M_CAP
Benign
0.034
D
MetaRNN
Benign
0.28
T;T
MetaSVM
Benign
-0.85
T
MutationAssessor
Benign
1.2
L;L
PrimateAI
Uncertain
0.72
T
PROVEAN
Benign
-0.81
N;N
REVEL
Benign
0.22
Sift
Benign
0.062
T;T
Sift4G
Benign
0.062
T;T
Polyphen
0.99
D;D
Vest4
0.35
MutPred
0.45
Gain of disorder (P = 0.0622);Gain of disorder (P = 0.0622);
MVP
0.33
MPC
1.4
ClinPred
0.70
D
GERP RS
-4.6
Varity_R
0.13
gMVP
0.63

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: rs141414055; hg19: chr9-95481034; API