9-92754144-CAAAA-CAAA

Variant names:

• chr9-92754144-CA-C
• rs59231772
• NM_001003800.2:c.240+10360delT

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1

The NM_001003800.2(BICD2):​c.240+10360delT variant causes a intron change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.40 (14367 hom., cov: 0)
• Consequence: BICD2 NM_001003800.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.267

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 Benign. Variant got -8 ACMG points.

• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.728 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
BICD2	NM_001003800.2	c.240+10360delT		intron_variant	Intron 1 of 6	ENST00000356884.11	NP_001003800.1
BICD2	NM_015250.4	c.240+10360delT		intron_variant	Intron 1 of 7		NP_056065.1
BICD2	XM_017014551.2	c.321+10279delT		intron_variant	Intron 1 of 7		XP_016870040.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
BICD2	ENST00000356884.11	c.240+10360delT		intron_variant	Intron 1 of 6	1	NM_001003800.2	ENSP00000349351.6
BICD2	ENST00000375512.3	c.240+10360delT		intron_variant	Intron 1 of 7	1		ENSP00000364662.3

Frequencies

GnomAD3 genomes AF: 0.403 AC: 56514 AN: 140120 Hom.: 14342 Cov.: 0

Gnomad AFR AF: 0.735

Gnomad AMI AF: 0.448

Gnomad AMR AF: 0.278

Gnomad ASJ AF: 0.357

Gnomad EAS AF: 0.00877

Gnomad SAS AF: 0.146

Gnomad FIN AF: 0.266

Gnomad MID AF: 0.473

Gnomad NFE AF: 0.300

Gnomad OTH AF: 0.397

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

GnomAD4 genome AF: 0.404 AC: 56553 AN: 140144 Hom.: 14367 Cov.: 0 AF XY: 0.394 AC XY: 26625 AN XY: 67606

Gnomad4 AFR AF: 0.736

Gnomad4 AMR AF: 0.278

Gnomad4 ASJ AF: 0.357

Gnomad4 EAS AF: 0.00880

Gnomad4 SAS AF: 0.144

Gnomad4 FIN AF: 0.266

Gnomad4 NFE AF: 0.300

Gnomad4 OTH AF: 0.394

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Other links and lift over

dbSNP: rs59231772; hg19: chr9-95516426;