dbSNP rs10844154: BICD1:c.426+11108A>C (chr12-32227567-A-C) – 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.426+11108A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.547 in 153,330 control chromosomes in the GnomAD database, including 23,797 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 0.55 ( 23585 hom., cov: 32)

Exomes 𝑓: 0.55 ( 212 hom. )

Consequence

BICD1
NM_001714.4 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 2.88

Publications

18 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:

ENSG00000258134 (HGNC:):

ENSG00000258134 links:

Genome browser will be placed here

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 (EAS) allele frequency at 95% confidence interval = 0.846 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
BICD1	NM_001714.4 link	c.426+11108A>C		intron_variant	Intron 2 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.426+11108A>C	intron_variant	Intron 2 of 9		NM_001714.4	ENSP00000498700.1	Q96G01-1
BICD1	ENST00000548411.6 link	c.426+11108A>C	intron_variant	Intron 2 of 8	1		ENSP00000446793.1	Q96G01-4
BICD1	ENST00000395758.3 link	n.426+11108A>C	intron_variant	Intron 2 of 9	1		ENSP00000379107.3	A8MVZ6
ENSG00000258134	ENST00000549976.1 link	n.588T>G	non_coding_transcript_exon_variant	Exon 1 of 1	6

Frequencies

GnomAD3 genomes

AF:

0.547

AC:

83077

AN:

151950

Hom.:

23565

Cov.:

show subpopulations

Gnomad AFR

AF:

0.424

Gnomad AMI

AF:

0.463

Gnomad AMR

AF:

0.651

Gnomad ASJ

AF:

0.510

Gnomad EAS

AF:

0.867

Gnomad SAS

AF:

0.718

Gnomad FIN

AF:

0.565

Gnomad MID

AF:

0.513

Gnomad NFE

AF:

0.561

Gnomad OTH

AF:

0.552

GnomAD4 exome

AF:

0.552

AC:

696

AN:

1262

Hom.:

212

Cov.:

AF XY:

0.523

AC XY:

343

AN XY:

656

show subpopulations

African (AFR)

AF:

0.250

AC:

AN:

American (AMR)

AF:

0.500

AC:

AN:

Ashkenazi Jewish (ASJ)

AF:

0.750

AC:

AN:

East Asian (EAS)

AF:

1.00

AC:

AN:

South Asian (SAS)

AF:

0.647

AC:

101

AN:

156

European-Finnish (FIN)

AF:

0.536

AC:

509

AN:

950

Middle Eastern (MID)

AF:

0.500

AC:

AN:

European-Non Finnish (NFE)

AF:

0.545

AC:

AN:

112

Other (OTH)

AF:

0.611

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.513

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

<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:

0.547

AC:

83136

AN:

152068

Hom.:

23585

Cov.:

AF XY:

0.553

AC XY:

41126

AN XY:

74336

show subpopulations

African (AFR)

AF:

0.424

AC:

17592

AN:

41470

American (AMR)

AF:

0.651

AC:

9958

AN:

15286

Ashkenazi Jewish (ASJ)

AF:

0.510

AC:

1772

AN:

3472

East Asian (EAS)

AF:

0.867

AC:

4480

AN:

5168

South Asian (SAS)

AF:

0.717

AC:

3456

AN:

4818

European-Finnish (FIN)

AF:

0.565

AC:

5983

AN:

10592

Middle Eastern (MID)

AF:

0.507

AC:

148

AN:

292

European-Non Finnish (NFE)

AF:

0.561

AC:

38152

AN:

67948

Other (OTH)

AF:

0.556

AC:

1174

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.505

Heterozygous variant carriers

1881

3762

5642

7523

9404

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

720

1440

2160

2880

3600

<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:

0.563

Hom.:

112138

Bravo

AF:

0.546

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.79

CADD

Benign

6.5

(source)

DANN

Benign

0.75

PhyloP100

2.9

Mutation Taster

=100/0

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