chr12-32246935-G-T

Variant names:

• chr12-32246935-G-T
• rs326641
• NM_001714.4:c.426+30476G>T

Variant summary

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

The NM_001714.4(BICD1):​c.426+30476G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.304 in 151,826 control chromosomes in the GnomAD database, including 7,877 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 0.30 (7877 hom., cov: 30)
• Consequence: BICD1 NM_001714.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.60
• Publications: 5 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=-0.77).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.389 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
BICD1	NM_001714.4	c.426+30476G>T		intron_variant	Intron 2 of 9	ENST00000652176.1	NP_001705.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
BICD1	ENST00000652176.1	c.426+30476G>T		intron_variant	Intron 2 of 9		NM_001714.4	ENSP00000498700.1
BICD1	ENST00000548411.6	c.426+30476G>T		intron_variant	Intron 2 of 8	1		ENSP00000446793.1
BICD1	ENST00000395758.3	n.426+30476G>T		intron_variant	Intron 2 of 9	1		ENSP00000379107.3

Frequencies

GnomAD3 genomes AF: 0.304 AC: 46192 AN: 151710 Hom.: 7880 Cov.: 30

Gnomad AFR AF: 0.156

Gnomad AMI AF: 0.333

Gnomad AMR AF: 0.298

Gnomad ASJ AF: 0.404

Gnomad EAS AF: 0.187

Gnomad SAS AF: 0.332

Gnomad FIN AF: 0.334

Gnomad MID AF: 0.383

Gnomad NFE AF: 0.393

Gnomad OTH AF: 0.305

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

GnomAD4 genome AF: 0.304 AC: 46187 AN: 151826 Hom.: 7877 Cov.: 30 AF XY: 0.301 AC XY: 22346 AN XY: 74182

African (AFR) AF: 0.156 AC: 6446 AN: 41416

American (AMR) AF: 0.297 AC: 4530 AN: 15230

Ashkenazi Jewish (ASJ) AF: 0.404 AC: 1399 AN: 3466

East Asian (EAS) AF: 0.188 AC: 969 AN: 5148

South Asian (SAS) AF: 0.334 AC: 1602 AN: 4800

European-Finnish (FIN) AF: 0.334 AC: 3522 AN: 10542

Middle Eastern (MID) AF: 0.384 AC: 113 AN: 294

European-Non Finnish (NFE) AF: 0.393 AC: 26672 AN: 67920

Other (OTH) AF: 0.300 AC: 630 AN: 2098

Alfa AF: 0.368 Hom.: 16547

Bravo AF: 0.292

Asia WGS AF: 0.242 AC: 843 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	6.0
DANN	Benign	0.86
PhyloP100		1.6
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: rs326641; hg19: chr12-32399869;