Genetic Variant BICD1:c.213+761A>G (chr12-32108305-A-G) – 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.213+761A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.601 in 195,220 control chromosomes in the GnomAD database, including 35,585 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 0.59 ( 26913 hom., cov: 32)

Exomes 𝑓: 0.63 ( 8672 hom. )

Consequence

BICD1
NM_001714.4 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.797

Publications

13 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:

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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 = 0.685 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
BICD1	NM_001714.4 link	c.213+761A>G		intron_variant	Intron 1 of 9	ENST00000652176.1	NP_001705.2	Q96G01-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
BICD1	ENST00000652176.1 link	c.213+761A>G		intron_variant	Intron 1 of 9		NM_001714.4	ENSP00000498700.1		Q96G01-1

Frequencies

GnomAD3 genomes

AF:

0.593

AC:

90048

AN:

151890

Hom.:

26880

Cov.:

show subpopulations

Gnomad AFR

AF:

0.564

Gnomad AMI

AF:

0.640

Gnomad AMR

AF:

0.696

Gnomad ASJ

AF:

0.645

Gnomad EAS

AF:

0.520

Gnomad SAS

AF:

0.633

Gnomad FIN

AF:

0.635

Gnomad MID

AF:

0.579

Gnomad NFE

AF:

0.580

Gnomad OTH

AF:

0.611

GnomAD4 exome

AF:

0.629

AC:

27169

AN:

43212

Hom.:

8672

Cov.:

AF XY:

0.634

AC XY:

13955

AN XY:

22028

show subpopulations

African (AFR)

AF:

0.604

AC:

723

AN:

1198

American (AMR)

AF:

0.733

AC:

2441

AN:

3332

Ashkenazi Jewish (ASJ)

AF:

0.678

AC:

853

AN:

1258

East Asian (EAS)

AF:

0.596

AC:

1671

AN:

2802

South Asian (SAS)

AF:

0.681

AC:

2623

AN:

3852

European-Finnish (FIN)

AF:

0.665

AC:

972

AN:

1462

Middle Eastern (MID)

AF:

0.585

AC:

AN:

142

European-Non Finnish (NFE)

AF:

0.608

AC:

16216

AN:

26656

Other (OTH)

AF:

0.632

AC:

1587

AN:

2510

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.522

Heterozygous variant carriers

501

1002

1503

2004

2505

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

174

348

522

696

870

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.593

AC:

90130

AN:

152008

Hom.:

26913

Cov.:

AF XY:

0.601

AC XY:

44619

AN XY:

74290

show subpopulations

African (AFR)

AF:

0.564

AC:

23376

AN:

41452

American (AMR)

AF:

0.696

AC:

10632

AN:

15266

Ashkenazi Jewish (ASJ)

AF:

0.645

AC:

2236

AN:

3468

East Asian (EAS)

AF:

0.520

AC:

2688

AN:

5166

South Asian (SAS)

AF:

0.634

AC:

3057

AN:

4818

European-Finnish (FIN)

AF:

0.635

AC:

6693

AN:

10546

Middle Eastern (MID)

AF:

0.575

AC:

169

AN:

294

European-Non Finnish (NFE)

AF:

0.580

AC:

39408

AN:

67974

Other (OTH)

AF:

0.609

AC:

1287

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1902

3804

5706

7608

9510

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

764

1528

2292

3056

3820

<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:

0.587

Hom.:

96574

Bravo

AF:

0.597

Asia WGS

AF:

0.598

AC:

2080

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.79

CADD

Benign

9.9

(source)

DANN

Benign

0.82

PhyloP100

0.80

Mutation Taster

=99/1

polymorphism (auto)

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over