9-92764654-G-T

Variant names:

• chr9-92764654-G-T
• NM_001003800.2:c.91C>A

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2 BP4_Moderate

The NM_001003800.2(BICD2):​c.91C>A​(p.His31Asn) variant causes a missense change. The variant allele was found at a frequency of 0.000000694 in 1,439,976 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts 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: 32)
  • Exomes 𝑓: 6.9e-7 (0 hom.)
• Consequence: BICD2 NM_001003800.2 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 6.08

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]

ACMG classification

Verdict is Uncertain_significance. Variant got 0 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.139182).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
BICD2	NM_001003800.2	c.91C>A	p.His31Asn	missense_variant	Exon 1 of 7	ENST00000356884.11	NP_001003800.1
BICD2	NM_015250.4	c.91C>A	p.His31Asn	missense_variant	Exon 1 of 8		NP_056065.1
BICD2	XM_017014551.2	c.91C>A	p.His31Asn	missense_variant	Exon 1 of 8		XP_016870040.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
BICD2	ENST00000356884.11	c.91C>A	p.His31Asn	missense_variant	Exon 1 of 7	1	NM_001003800.2	ENSP00000349351.6
BICD2	ENST00000375512.3	c.91C>A	p.His31Asn	missense_variant	Exon 1 of 8	1		ENSP00000364662.3

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome AF: 6.94e-7 AC: 1 AN: 1439976 Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0 AN XY: 714868

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: 0.0000204

Gnomad4 NFE exome AF: 0.00

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.089
BayesDel_addAF	Benign	-0.17	T
BayesDel_noAF	Benign	-0.48
CADD	Pathogenic	26
DANN	Benign	0.96
DEOGEN2	Benign	0.031	.;T
Eigen	Benign	-0.24
Eigen_PC	Benign	-0.025
FATHMM_MKL	Uncertain	0.93	D
LIST_S2	Benign	0.63	T;T
M_CAP	Uncertain	0.14	D
MetaRNN	Benign	0.14	T;T
MetaSVM	Benign	-1.1	T
MutationAssessor	Benign	0.0	N;N
PrimateAI	Pathogenic	0.85	D
PROVEAN	Benign	0.16	N;N
REVEL	Benign	0.081
Sift	Benign	0.23	T;T
Sift4G	Benign	0.21	T;T
Polyphen		0.017	B;B
Vest4		0.29
MutPred		0.13		Gain of ubiquitination at K27 (P = 0.0743);Gain of ubiquitination at K27 (P = 0.0743);
MVP		0.65
MPC		0.68
ClinPred		0.72	D
GERP RS		4.7
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1
Varity_R		0.31
gMVP		0.14

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

No publications associated with this variant yet.

Other links and lift over

hg19: chr9-95526936;