chr9-92720550-AAGGA-GAGTC

Variant names:

• chr9-92720550-AAGGA-GAGTC
• NM_001003800.2:c.808_812delTCCTTinsGACTC

Variant summary

Our verdict is Uncertain significance. Variant got 3 ACMG points: 3P and 0B. PM2 PP3

The NM_001003800.2(BICD2):​c.808_812delTCCTTinsGACTC​(p.SerPhe270AspSer) variant causes a missense change involving the alteration of a conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: not found (cov: 33)
• Consequence: BICD2 NM_001003800.2 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 7.96

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 3 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• PP3: No computational evidence supports a deleterious effect, but strongly conserved according to phyloP

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
BICD2	NM_001003800.2	c.808_812delTCCTTinsGACTC	p.SerPhe270AspSer	missense_variant		ENST00000356884.11	NP_001003800.1
BICD2	NM_015250.4	c.808_812delTCCTTinsGACTC	p.SerPhe270AspSer	missense_variant			NP_056065.1
BICD2	XM_017014551.2	c.889_893delTCCTTinsGACTC	p.SerPhe297AspSer	missense_variant			XP_016870040.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
BICD2	ENST00000356884.11	c.808_812delTCCTTinsGACTC	p.SerPhe270AspSer	missense_variant		1	NM_001003800.2	ENSP00000349351.6
BICD2	ENST00000375512.3	c.808_812delTCCTTinsGACTC	p.SerPhe270AspSer	missense_variant		1		ENSP00000364662.3

Frequencies

GnomAD3 genomes Cov.: 33

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome Cov.: 33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Splicing

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: chr9-95482832;