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_001413182.1(BICD1):c.*617A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.601 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_001413182.1 3_prime_UTR

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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001413182.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
BICD1	NM_001714.4	MANE Select	c.213+761A>G	intron	N/A	NP_001705.2
BICD1	NM_001413182.1		c.*617A>G	3_prime_UTR	Exon 2 of 2	NP_001400111.1
BICD1	NM_001413183.1		c.*394A>G	3_prime_UTR	Exon 2 of 2	NP_001400112.1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
BICD1	ENST00000652176.1	MANE Select	c.213+761A>G	intron	N/A	ENSP00000498700.1
BICD1	ENST00000548411.6	TSL:1	c.213+761A>G	intron	N/A	ENSP00000446793.1
BICD1	ENST00000395758.3	TSL:1	n.213+761A>G	intron	N/A	ENSP00000379107.3

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 v4.9

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

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over