rs155202

Variant names:

• chr12-32353923-G-A
• rs155202
• NM_001714.4:c.2765-13747G>A

Variant summary

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

The NM_001714.4(BICD1):​c.2765-13747G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.444 in 151,922 control chromosomes in the GnomAD database, including 16,295 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 0.44 (16295 hom., cov: 31)
  • Failed GnomAD Quality Control
• Consequence: BICD1 NM_001714.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.331
• 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]

ENSG00000276115 (HGNC:):

ACMG classification

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 = 0.56 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
BICD1	NM_001714.4	c.2765-13747G>A		intron_variant	Intron 8 of 9	ENST00000652176.1	NP_001705.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
BICD1	ENST00000652176.1	c.2765-13747G>A		intron_variant	Intron 8 of 9		NM_001714.4	ENSP00000498700.1
BICD1	ENST00000548411.6	c.2461-13747G>A		intron_variant	Intron 7 of 8	1		ENSP00000446793.1
BICD1	ENST00000395758.3	n.*171-13747G>A		intron_variant	Intron 8 of 9	1		ENSP00000379107.3
ENSG00000276115	ENST00000614539.1	n.1575G>A		non_coding_transcript_exon_variant	Exon 1 of 1	6

Frequencies

GnomAD3 genomes AF: 0.444 AC: 67436 AN: 151804 Hom.: 16284 Cov.: 31

Gnomad AFR AF: 0.241

Gnomad AMI AF: 0.544

Gnomad AMR AF: 0.569

Gnomad ASJ AF: 0.490

Gnomad EAS AF: 0.536

Gnomad SAS AF: 0.539

Gnomad FIN AF: 0.517

Gnomad MID AF: 0.439

Gnomad NFE AF: 0.511

Gnomad OTH AF: 0.444

GnomAD4 exome Data not reliable, filtered out with message: AC0 AC: 0 AN: 0 Hom.: 0 Cov.: 0 AC XY: 0 AN XY: 0

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AC: 0 AN: 0

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.444 AC: 67484 AN: 151922 Hom.: 16295 Cov.: 31 AF XY: 0.447 AC XY: 33206 AN XY: 74252

African (AFR) AF: 0.242 AC: 10017 AN: 41468

American (AMR) AF: 0.570 AC: 8696 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.490 AC: 1699 AN: 3466

East Asian (EAS) AF: 0.536 AC: 2766 AN: 5164

South Asian (SAS) AF: 0.539 AC: 2592 AN: 4808

European-Finnish (FIN) AF: 0.517 AC: 5448 AN: 10538

Middle Eastern (MID) AF: 0.438 AC: 128 AN: 292

European-Non Finnish (NFE) AF: 0.511 AC: 34704 AN: 67908

Other (OTH) AF: 0.446 AC: 939 AN: 2106

Alfa AF: 0.495 Hom.: 32416

Bravo AF: 0.439

Asia WGS AF: 0.528 AC: 1833 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	6.4
DANN	Benign	0.52
PhyloP100		-0.33
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs155202; hg19: chr12-32506857;