Variant 12-32107615-CAAG-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP6_ModerateBS2

The NM_001714.4(BICD1):c.213+75_213+77delAAG variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00739 in 1,462,370 control chromosomes in the GnomAD database, including 64 homozygotes. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.0060 ( 6 hom., cov: 32)

Exomes 𝑓: 0.0075 ( 58 hom. )

Consequence

BICD1
NM_001714.4 intron

Scores

Not classified

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: 2.22

Variant links:

Genes affected

BICD1 (HGNC:1049): (BICD cargo adaptor 1) This gene encodes an adaptor protein that belongs to the bicaudal D family of dynein cargo adaptors. The encoded protein acts as an intracellular cargo transport cofactor that regulates the microtubule-based loading of cargo onto the dynein motor complex. It also controls dynein motor activity and coordination. It has a domain architecture consisting of coiled-coil domains at the N- and C-termini that are highly conserved in other family members. Naturally occurring mutations in this gene are associated with short telomere length and emphysema. [provided by RefSeq, Aug 2017]

BICD1 links:

BICD1 (HGNC:):

BICD1 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -6 ACMG points.

BP6

Variant 12-32107615-CAAG-C is Benign according to our data. Variant chr12-32107615-CAAG-C is described in ClinVar as [Likely_benign]. Clinvar id is 2642834.Status of the report is criteria_provided_single_submitter, 1 stars.

BS2

High Homozygotes in GnomAd4 at 6 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
BICD1	NM_001714.4 linkuse as main transcript	c.213+75_213+77delAAG		intron_variant		ENST00000652176.1	NP_001705.2	Q96G01-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
BICD1	ENST00000652176.1 linkuse as main transcript	c.213+75_213+77delAAG		intron_variant			NM_001714.4	ENSP00000498700.1		Q96G01-1

Frequencies

GnomAD3 genomes

AF:

0.00602

AC:

916

AN:

152142

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00138

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00419

Gnomad ASJ

AF:

0.0418

Gnomad EAS

AF:

0.000192

Gnomad SAS

AF:

0.00394

Gnomad FIN

AF:

0.00311

Gnomad MID

AF:

0.0127

Gnomad NFE

AF:

0.00850

Gnomad OTH

AF:

0.00717

GnomAD3 exomes

AF:

0.00764

AC:

1097

AN:

143658

Hom.:

AF XY:

0.00785

AC XY:

601

AN XY:

76588

show subpopulations

Gnomad AFR exome

AF:

0.00143

Gnomad AMR exome

AF:

0.00365

Gnomad ASJ exome

AF:

0.0446

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.00458

Gnomad FIN exome

AF:

0.00326

Gnomad NFE exome

AF:

0.00815

Gnomad OTH exome

AF:

0.00770

GnomAD4 exome

AF:

0.00755

AC:

9885

AN:

1310110

Hom.:

AF XY:

0.00758

AC XY:

4931

AN XY:

650800

show subpopulations

Gnomad4 AFR exome

AF:

0.00144

Gnomad4 AMR exome

AF:

0.00340

Gnomad4 ASJ exome

AF:

0.0465

Gnomad4 EAS exome

AF:

0.0000283

Gnomad4 SAS exome

AF:

0.00458

Gnomad4 FIN exome

AF:

0.00417

Gnomad4 NFE exome

AF:

0.00751

Gnomad4 OTH exome

AF:

0.00832

GnomAD4 genome

AF:

0.00601

AC:

915

AN:

152260

Hom.:

Cov.:

AF XY:

0.00575

AC XY:

428

AN XY:

74450

show subpopulations

Gnomad4 AFR

AF:

0.00137

Gnomad4 AMR

AF:

0.00419

Gnomad4 ASJ

AF:

0.0418

Gnomad4 EAS

AF:

0.000193

Gnomad4 SAS

AF:

0.00395

Gnomad4 FIN

AF:

0.00311

Gnomad4 NFE

AF:

0.00850

Gnomad4 OTH

AF:

0.00710

Alfa

AF:

0.0109

Hom.:

Bravo

AF:

0.00573

Asia WGS

AF:

0.00231

AC:

AN:

3478

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Likely benign, criteria provided, single submitter

clinical testing

CeGaT Center for Human Genetics Tuebingen

Dec 01, 2022

BICD1: BS2 -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.030

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over