12-32308023-G-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001714.4(BICD1):c.1005+1901G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.823 in 152,196 control chromosomes in the GnomAD database, including 52,054 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 0.82 (52054 hom., cov: 32)
• Consequence: BICD1 NM_001714.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0870

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.867 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
BICD1	NM_001714.4	c.1005+1901G>C		intron_variant		ENST00000652176.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
BICD1	ENST00000652176.1	c.1005+1901G>C		intron_variant			NM_001714.4	A1
BICD1	ENST00000548411.6	c.1005+1901G>C		intron_variant		1		P4
BICD1	ENST00000395758.3	c.1005+1901G>C		intron_variant, NMD_transcript_variant		1

Frequencies

GnomAD3 genomes AF: 0.824 AC: 125251 AN: 152078 Hom.: 52022 Cov.: 32

Gnomad AFR AF: 0.834

Gnomad AMI AF: 0.805

Gnomad AMR AF: 0.684

Gnomad ASJ AF: 0.838

Gnomad EAS AF: 0.599

Gnomad SAS AF: 0.716

Gnomad FIN AF: 0.823

Gnomad MID AF: 0.810

Gnomad NFE AF: 0.873

Gnomad OTH AF: 0.823

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

GnomAD4 genome AF: 0.823 AC: 125322 AN: 152196 Hom.: 52054 Cov.: 32 AF XY: 0.814 AC XY: 60550 AN XY: 74402

Gnomad4 AFR AF: 0.834

Gnomad4 AMR AF: 0.683

Gnomad4 ASJ AF: 0.838

Gnomad4 EAS AF: 0.599

Gnomad4 SAS AF: 0.717

Gnomad4 FIN AF: 0.823

Gnomad4 NFE AF: 0.873

Gnomad4 OTH AF: 0.818

Alfa AF: 0.848 Hom.: 6430

Bravo AF: 0.811

Asia WGS AF: 0.642 AC: 2237 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
Cadd	Benign	4.3
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

Other links and lift over

dbSNP: rs2650128; hg19: chr12-32460957;