9-92754144-CAAAA-CA

Variant names:

• chr9-92754144-CAAA-C
• rs59231772
• NM_001003800.2:c.240+10358_240+10360delTTT

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BS1 BS2

The NM_001003800.2(BICD2):​c.240+10358_240+10360delTTT 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 0.00035 (0 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.

• BS1: Variant frequency is greater than expected in population eas. gnomad4 allele frequency = 0.000349 (49/140344) while in subpopulation EAS AF= 0.000628 (3/4778). AF 95% confidence interval is 0.000232. There are 0 homozygotes in gnomad4. There are 28 alleles in male gnomad4 subpopulation. Median coverage is 0. This position pass quality control queck.
• BS2: High AC in GnomAd4 at 49 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
BICD2	NM_001003800.2	c.240+10358_240+10360delTTT		intron_variant	Intron 1 of 6	ENST00000356884.11	NP_001003800.1
BICD2	NM_015250.4	c.240+10358_240+10360delTTT		intron_variant	Intron 1 of 7		NP_056065.1
BICD2	XM_017014551.2	c.321+10277_321+10279delTTT		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+10358_240+10360delTTT		intron_variant	Intron 1 of 6	1	NM_001003800.2	ENSP00000349351.6
BICD2	ENST00000375512.3	c.240+10358_240+10360delTTT		intron_variant	Intron 1 of 7	1		ENSP00000364662.3

Frequencies

GnomAD3 genomes AF: 0.000349 AC: 49 AN: 140322 Hom.: 0 Cov.: 0

Gnomad AFR AF: 0.000157

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000426

Gnomad ASJ AF: 0.000298

Gnomad EAS AF: 0.000626

Gnomad SAS AF: 0.000224

Gnomad FIN AF: 0.00121

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.000344

Gnomad OTH AF: 0.00

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

GnomAD4 genome AF: 0.000349 AC: 49 AN: 140344 Hom.: 0 Cov.: 0 AF XY: 0.000414 AC XY: 28 AN XY: 67712

Gnomad4 AFR AF: 0.000157

Gnomad4 AMR AF: 0.000426

Gnomad4 ASJ AF: 0.000298

Gnomad4 EAS AF: 0.000628

Gnomad4 SAS AF: 0.000225

Gnomad4 FIN AF: 0.00121

Gnomad4 NFE AF: 0.000344

Gnomad4 OTH AF: 0.00

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;