rs11064994

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001367886.1(BICDL1):​c.645+19224A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0442 in 152,236 control chromosomes in the GnomAD database, including 227 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 0.044 ( 227 hom., cov: 32)

Consequence

BICDL1
NM_001367886.1 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.862
Variant links:
Genes affected
BICDL1 (HGNC:28095): (BICD family like cargo adaptor 1) Predicted to enable dynactin binding activity and small GTPase binding activity. Predicted to be involved in Golgi to secretory granule transport; neuron projection development; and vesicle transport along microtubule. Predicted to be located in centrosome. [provided by Alliance of Genome Resources, Apr 2022]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.89).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0703 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
BICDL1NM_001367886.1 linkuse as main transcriptc.645+19224A>G intron_variant ENST00000548673.6

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
BICDL1ENST00000548673.6 linkuse as main transcriptc.645+19224A>G intron_variant 2 NM_001367886.1 A1
BICDL1ENST00000546420.5 linkuse as main transcriptc.*101+18048A>G intron_variant, NMD_transcript_variant 1
BICDL1ENST00000397558.6 linkuse as main transcriptc.645+19224A>G intron_variant 5 P4Q6ZP65-1

Frequencies

GnomAD3 genomes
AF:
0.0442
AC:
6726
AN:
152118
Hom.:
227
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0119
Gnomad AMI
AF:
0.0471
Gnomad AMR
AF:
0.0336
Gnomad ASJ
AF:
0.0444
Gnomad EAS
AF:
0.000577
Gnomad SAS
AF:
0.0298
Gnomad FIN
AF:
0.0366
Gnomad MID
AF:
0.0316
Gnomad NFE
AF:
0.0720
Gnomad OTH
AF:
0.0407
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.0442
AC:
6727
AN:
152236
Hom.:
227
Cov.:
32
AF XY:
0.0412
AC XY:
3070
AN XY:
74438
show subpopulations
Gnomad4 AFR
AF:
0.0118
Gnomad4 AMR
AF:
0.0335
Gnomad4 ASJ
AF:
0.0444
Gnomad4 EAS
AF:
0.000578
Gnomad4 SAS
AF:
0.0304
Gnomad4 FIN
AF:
0.0366
Gnomad4 NFE
AF:
0.0720
Gnomad4 OTH
AF:
0.0403
Alfa
AF:
0.0639
Hom.:
726
Bravo
AF:
0.0411
Asia WGS
AF:
0.0150
AC:
52
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.89
CADD
Benign
2.0
DANN
Benign
0.65

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.

Other links and lift over

dbSNP: rs11064994; hg19: chr12-120455764; API