dbSNP rs3748275: BICD1:p.Val568Val (chr12-32328159-G-C) – ACMG Classification: Benign (-21 pts)

Variant summary

Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1

The NM_001714.4(BICD1):c.1704G>C(p.Val568Val) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.223 in 1,613,888 control chromosomes in the GnomAD database, including 45,181 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.22 ( 4157 hom., cov: 31)

Exomes 𝑓: 0.22 ( 41024 hom. )

Consequence

BICD1
NM_001714.4 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: 0.847

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:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -21 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.47).

BP6

Variant 12-32328159-G-C is Benign according to our data. Variant chr12-32328159-G-C is described in ClinVar as [Benign]. Clinvar id is 402425.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=0.847 with no splicing effect.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.58 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
BICD1	NM_001714.4 link	c.1704G>C	p.Val568Val	synonymous_variant	Exon 5 of 10	ENST00000652176.1	NP_001705.2	Q96G01-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	UniProt
BICD1	ENST00000652176.1 link	c.1704G>C	p.Val568Val	synonymous_variant	Exon 5 of 10		NM_001714.4	ENSP00000498700.1	Q96G01-1
BICD1	ENST00000548411.6 link	c.1704G>C	p.Val568Val	synonymous_variant	Exon 5 of 9	1		ENSP00000446793.1	Q96G01-4
BICD1	ENST00000395758.3 link	n.1704G>C		non_coding_transcript_exon_variant	Exon 5 of 10	1		ENSP00000379107.3	A8MVZ6
BICD1	ENST00000547680.2 link	c.-244G>C		upstream_gene_variant		3		ENSP00000475837.1	U3KQF7

Frequencies

GnomAD3 genomes

AF:

0.217

AC:

33038

AN:

151922

Hom.:

4150

Cov.:

show subpopulations

Gnomad AFR

AF:

0.152

Gnomad AMI

AF:

0.206

Gnomad AMR

AF:

0.207

Gnomad ASJ

AF:

0.164

Gnomad EAS

AF:

0.598

Gnomad SAS

AF:

0.184

Gnomad FIN

AF:

0.322

Gnomad MID

AF:

0.0791

Gnomad NFE

AF:

0.221

Gnomad OTH

AF:

0.214

GnomAD3 exomes

AF:

0.238

AC:

59742

AN:

251248

Hom.:

8599

AF XY:

0.235

AC XY:

31879

AN XY:

135804

show subpopulations

Gnomad AFR exome

AF:

0.148

Gnomad AMR exome

AF:

0.195

Gnomad ASJ exome

AF:

0.165

Gnomad EAS exome

AF:

0.600

Gnomad SAS exome

AF:

0.169

Gnomad FIN exome

AF:

0.315

Gnomad NFE exome

AF:

0.217

Gnomad OTH exome

AF:

0.218

GnomAD4 exome

AF:

0.224

AC:

326850

AN:

1461848

Hom.:

41024

Cov.:

AF XY:

0.222

AC XY:

161129

AN XY:

727228

show subpopulations

Gnomad4 AFR exome

AF:

0.154

Gnomad4 AMR exome

AF:

0.193

Gnomad4 ASJ exome

AF:

0.162

Gnomad4 EAS exome

AF:

0.653

Gnomad4 SAS exome

AF:

0.170

Gnomad4 FIN exome

AF:

0.311

Gnomad4 NFE exome

AF:

0.214

Gnomad4 OTH exome

AF:

0.218

GnomAD4 genome

AF:

0.218

AC:

33078

AN:

152040

Hom.:

4157

Cov.:

AF XY:

0.224

AC XY:

16657

AN XY:

74282

show subpopulations

Gnomad4 AFR

AF:

0.152

Gnomad4 AMR

AF:

0.207

Gnomad4 ASJ

AF:

0.164

Gnomad4 EAS

AF:

0.597

Gnomad4 SAS

AF:

0.185

Gnomad4 FIN

AF:

0.322

Gnomad4 NFE

AF:

0.221

Gnomad4 OTH

AF:

0.217

Alfa

AF:

0.216

Hom.:

1196

Bravo

AF:

0.210

Asia WGS

AF:

0.327

AC:

1136

AN:

3478

EpiCase

AF:

0.211

EpiControl

AF:

0.203

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not specified

Benign:1

Mar 28, 2016

Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

Variant identified in a genome or exome case(s) and assessed due to predicted null impact of the variant or pathogenic assertions in the literature or databases. Disclaimer: This variant has not undergone full assessment. The following are preliminary notes: MAF -

not provided

Benign:1

Breakthrough Genomics, Breakthrough Genomics

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: not provided

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.47

CADD

Benign

5.2

DANN

Benign

0.69

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

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