rs1151026

Variant names:

• chr12-32176235-A-G
• rs1151026
• NM_001714.4:c.214-40012A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001714.4(BICD1):​c.214-40012A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.147 in 152,120 control chromosomes in the GnomAD database, including 1,918 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 0.15 (1918 hom., cov: 32)
• Consequence: BICD1 NM_001714.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.249
• Publications: 4 publications found

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]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.204 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
BICD1	NM_001714.4	c.214-40012A>G		intron_variant	Intron 1 of 9	ENST00000652176.1	NP_001705.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
BICD1	ENST00000652176.1	c.214-40012A>G		intron_variant	Intron 1 of 9		NM_001714.4	ENSP00000498700.1
BICD1	ENST00000548411.6	c.214-40012A>G		intron_variant	Intron 1 of 8	1		ENSP00000446793.1
BICD1	ENST00000395758.3	n.214-40012A>G		intron_variant	Intron 1 of 9	1		ENSP00000379107.3

Frequencies

GnomAD3 genomes AF: 0.147 AC: 22316 AN: 152002 Hom.: 1917 Cov.: 32

Gnomad AFR AF: 0.0715

Gnomad AMI AF: 0.188

Gnomad AMR AF: 0.0944

Gnomad ASJ AF: 0.144

Gnomad EAS AF: 0.214

Gnomad SAS AF: 0.156

Gnomad FIN AF: 0.124

Gnomad MID AF: 0.108

Gnomad NFE AF: 0.202

Gnomad OTH AF: 0.128

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.147 AC: 22327 AN: 152120 Hom.: 1918 Cov.: 32 AF XY: 0.141 AC XY: 10472 AN XY: 74370

African (AFR) AF: 0.0714 AC: 2965 AN: 41500

American (AMR) AF: 0.0943 AC: 1440 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.144 AC: 500 AN: 3470

East Asian (EAS) AF: 0.215 AC: 1113 AN: 5180

South Asian (SAS) AF: 0.156 AC: 752 AN: 4816

European-Finnish (FIN) AF: 0.124 AC: 1311 AN: 10572

Middle Eastern (MID) AF: 0.116 AC: 34 AN: 294

European-Non Finnish (NFE) AF: 0.202 AC: 13767 AN: 67988

Other (OTH) AF: 0.130 AC: 274 AN: 2114

Alfa AF: 0.179 Hom.: 3713

Bravo AF: 0.141

Asia WGS AF: 0.191 AC: 663 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	7.2
DANN	Benign	0.69
PhyloP100		-0.25
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs1151026; hg19: chr12-32329169;