12-32143765-G-T

Variant names:

• chr12-32143765-G-T
• rs10771917
• NM_001714.4:c.213+36221G>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.213+36221G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.818 in 152,110 control chromosomes in the GnomAD database, including 51,011 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 (51011 hom., cov: 32)
• Consequence: BICD1 NM_001714.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.176
• Publications: 1 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=-0.93).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.877 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001714.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	BICD1	NM_001714.4	MANE Select	c.213+36221G>T		intron	N/A	NP_001705.2
	BICD1	NM_001413156.1		c.213+36221G>T		intron	N/A	NP_001400085.1
	BICD1	NM_001413157.1		c.213+36221G>T		intron	N/A	NP_001400086.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	BICD1	ENST00000652176.1	MANE Select	c.213+36221G>T		intron	N/A	ENSP00000498700.1
	BICD1	ENST00000548411.6	TSL:1	c.213+36221G>T		intron	N/A	ENSP00000446793.1
	BICD1	ENST00000395758.3	TSL:1	n.213+36221G>T		intron	N/A	ENSP00000379107.3

Frequencies

GnomAD3 genomes AF: 0.818 AC: 124357 AN: 151992 Hom.: 50987 Cov.: 32

Gnomad AFR AF: 0.776

Gnomad AMI AF: 0.804

Gnomad AMR AF: 0.889

Gnomad ASJ AF: 0.863

Gnomad EAS AF: 0.785

Gnomad SAS AF: 0.846

Gnomad FIN AF: 0.883

Gnomad MID AF: 0.892

Gnomad NFE AF: 0.815

Gnomad OTH AF: 0.850

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

GnomAD4 genome AF: 0.818 AC: 124428 AN: 152110 Hom.: 51011 Cov.: 32 AF XY: 0.825 AC XY: 61326 AN XY: 74378

African (AFR) AF: 0.776 AC: 32172 AN: 41476

American (AMR) AF: 0.889 AC: 13594 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.863 AC: 2994 AN: 3470

East Asian (EAS) AF: 0.784 AC: 4063 AN: 5182

South Asian (SAS) AF: 0.846 AC: 4075 AN: 4818

European-Finnish (FIN) AF: 0.883 AC: 9343 AN: 10584

Middle Eastern (MID) AF: 0.888 AC: 261 AN: 294

European-Non Finnish (NFE) AF: 0.815 AC: 55409 AN: 67978

Other (OTH) AF: 0.845 AC: 1784 AN: 2110

Alfa AF: 0.780 Hom.: 3605

Bravo AF: 0.817

Asia WGS AF: 0.787 AC: 2738 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.86
DANN	Benign	0.53
PhyloP100		-0.18
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: rs10771917; hg19: chr12-32296699;