Genetic Variant NM_001714.4:c.2765-13747G>A (chr12-32353923-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001714.4(BICD1):c.2765-13747G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.444 in 151,922 control chromosomes in the GnomAD database, including 16,295 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.44 ( 16295 hom., cov: 31)

Failed GnomAD Quality Control

Consequence

BICD1
NM_001714.4 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.331

Publications

4 publications found

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:

ENSG00000276115 (HGNC:):

ENSG00000276115 links:

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.79).

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.56 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
BICD1	NM_001714.4 link	c.2765-13747G>A		intron_variant	Intron 8 of 9	ENST00000652176.1	NP_001705.2	Q96G01-1

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein	UniProt
BICD1	ENST00000652176.1 link	c.2765-13747G>A	intron_variant	Intron 8 of 9		NM_001714.4	ENSP00000498700.1	Q96G01-1
BICD1	ENST00000548411.6 link	c.2461-13747G>A	intron_variant	Intron 7 of 8	1		ENSP00000446793.1	Q96G01-4
BICD1	ENST00000395758.3 link	n.*171-13747G>A	intron_variant	Intron 8 of 9	1		ENSP00000379107.3	A8MVZ6
ENSG00000276115	ENST00000614539.1 link	n.1575G>A	non_coding_transcript_exon_variant	Exon 1 of 1	6

Frequencies

GnomAD3 genomes

AF:

0.444

AC:

67436

AN:

151804

Hom.:

16284

Cov.:

show subpopulations

Gnomad AFR

AF:

0.241

Gnomad AMI

AF:

0.544

Gnomad AMR

AF:

0.569

Gnomad ASJ

AF:

0.490

Gnomad EAS

AF:

0.536

Gnomad SAS

AF:

0.539

Gnomad FIN

AF:

0.517

Gnomad MID

AF:

0.439

Gnomad NFE

AF:

0.511

Gnomad OTH

AF:

0.444

GnomAD4 exome

Data not reliable, filtered out with message: AC0

AC:

AN:

Hom.:

Cov.:

AC XY:

AN XY:

African (AFR)

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AC:

AN:

Other (OTH)

AC:

AN:

GnomAD4 genome

AF:

0.444

AC:

67484

AN:

151922

Hom.:

16295

Cov.:

AF XY:

0.447

AC XY:

33206

AN XY:

74252

show subpopulations

African (AFR)

AF:

0.242

AC:

10017

AN:

41468

American (AMR)

AF:

0.570

AC:

8696

AN:

15262

Ashkenazi Jewish (ASJ)

AF:

0.490

AC:

1699

AN:

3466

East Asian (EAS)

AF:

0.536

AC:

2766

AN:

5164

South Asian (SAS)

AF:

0.539

AC:

2592

AN:

4808

European-Finnish (FIN)

AF:

0.517

AC:

5448

AN:

10538

Middle Eastern (MID)

AF:

0.438

AC:

128

AN:

292

European-Non Finnish (NFE)

AF:

0.511

AC:

34704

AN:

67908

Other (OTH)

AF:

0.446

AC:

939

AN:

2106

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1796

3592

5387

7183

8979

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

630

1260

1890

2520

3150

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.495

Hom.:

32416

Bravo

AF:

0.439

Asia WGS

AF:

0.528

AC:

1833

AN:

3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.79

CADD

Benign

6.4

(source)

DANN

Benign

0.52

PhyloP100

-0.33

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.010

Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over