chr9-92713365-G-T

Position:

• chr9-92713365-G-T

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_Strong BP6_Very_Strong BA1

The NM_001003800.2(BICD2):​c.*1789C>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0737 in 1,393,078 control chromosomes in the GnomAD database, including 4,314 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

• Frequency:
  • Genomes: 𝑓 0.060 (389 hom., cov: 33)
  • Exomes 𝑓: 0.075 (3925 hom.)
• Consequence: BICD2 NM_001003800.2 3_prime_UTR
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:2
• Conservation: PhyloP100: 1.72

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 -20 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.48).
• BP6: Variant 9-92713365-G-T is Benign according to our data. Variant chr9-92713365-G-T is described in ClinVar as [Benign]. Clinvar id is 1261177.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.088 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
BICD2	NM_001003800.2	c.*1789C>A		3_prime_UTR_variant	7/7	ENST00000356884.11
BICD2	NM_015250.4	c.*91C>A		3_prime_UTR_variant	8/8
BICD2	XM_017014551.2	c.*91C>A		3_prime_UTR_variant	8/8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
BICD2	ENST00000356884.11	c.*1789C>A		3_prime_UTR_variant	7/7	1	NM_001003800.2	A2
BICD2	ENST00000375512.3	c.*91C>A		3_prime_UTR_variant	8/8	1		P4

Frequencies

GnomAD3 genomes AF: 0.0598 AC: 9097 AN: 152168 Hom.: 388 Cov.: 33

Gnomad AFR AF: 0.0147

Gnomad AMI AF: 0.127

Gnomad AMR AF: 0.0599

Gnomad ASJ AF: 0.113

Gnomad EAS AF: 0.000385

Gnomad SAS AF: 0.0292

Gnomad FIN AF: 0.0493

Gnomad MID AF: 0.231

Gnomad NFE AF: 0.0899

Gnomad OTH AF: 0.103

GnomAD4 exome AF: 0.0754 AC: 93509 AN: 1240792 Hom.: 3925 Cov.: 19 AF XY: 0.0749 AC XY: 45983 AN XY: 613900

Gnomad4 AFR exome AF: 0.0140

Gnomad4 AMR exome AF: 0.0488

Gnomad4 ASJ exome AF: 0.116

Gnomad4 EAS exome AF: 0.000201

Gnomad4 SAS exome AF: 0.0359

Gnomad4 FIN exome AF: 0.0520

Gnomad4 NFE exome AF: 0.0839

Gnomad4 OTH exome AF: 0.0771

GnomAD4 genome AF: 0.0597 AC: 9095 AN: 152286 Hom.: 389 Cov.: 33 AF XY: 0.0574 AC XY: 4272 AN XY: 74472

Gnomad4 AFR AF: 0.0147

Gnomad4 AMR AF: 0.0599

Gnomad4 ASJ AF: 0.113

Gnomad4 EAS AF: 0.000386

Gnomad4 SAS AF: 0.0294

Gnomad4 FIN AF: 0.0493

Gnomad4 NFE AF: 0.0898

Gnomad4 OTH AF: 0.102

Alfa AF: 0.0763 Hom.: 86

Bravo AF: 0.0598

Asia WGS AF: 0.0180 AC: 64 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

not provided Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	Jun 28, 2018	- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.48
CADD	Benign	15
DANN	Benign	0.88

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: rs10992429; hg19: chr9-95475647;