3-45942808-C-G

Variant names:

• chr3-45942808-C-G
• rs2234350
• NM_024513.4:c.3945-6265G>C

Variant summary

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

The NM_024513.4(FYCO1):​c.3945-6265G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.787 in 152,246 control chromosomes in the GnomAD database, including 47,676 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 0.79 (47676 hom., cov: 33)
• Consequence: FYCO1 NM_024513.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0900
• Publications: 6 publications found

Genes affected

FYCO1 (HGNC:14673): (FYVE and coiled-coil domain autophagy adaptor 1) The gene encodes a Rab7 adapter protein that is implicated in the microtubule transport of autophagosomes. The encoded protein contains a RUN domain, a FYVE-type zinc finger domain, and Golgi dynamics (GOLD) domain. The encoded protein plays a role in microtubule plus end-directed transport of autophagic vesicles through interactions with the small GTPase Rab7, phosphatidylinositol-3-phosphate (PI3P), the autophagosome marker LC3, and the kinesin KIF5. Mutations in this gene are associated with inclusion body myositis (IBM) and autosomal recessive congenital cataracts (CATC2). [provided by RefSeq, Aug 2020]

CXCR6 (HGNC:16647): (C-X-C motif chemokine receptor 6) The protein encoded by this gene is a G protein-coupled receptor with seven transmembrane domains that belongs to the CXC chemokine receptor family. This family also includes CXCR1, CXCR2, CXCR3, CXCR4, CXCR5, and CXCR7. This gene, which maps to the chemokine receptor gene cluster, is expressed in several T lymphocyte subsets and bone marrow stromal cells. The encoded protein and its exclusive ligand, chemokine ligand 16 (CCL16), are part of a signalling pathway that regulates T lymphocyte migration to various peripheral tissues (the liver, spleen red pulp, intestine, lungs, and skin) and promotes cell-cell interaction with dendritic cells and fibroblastic reticular cells. CXCR6/CCL16 also controls the localization of resident memory T lymphocytes to different compartments of the lung and maintains airway resident memory T lymphocytes, which are an important first line of defense against respiratory pathogens. The encoded protein serves as an entry coreceptor used by HIV-1 and SIV to enter target cells, in conjunction with CD4. [provided by RefSeq, Aug 2020]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.937 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
FYCO1	NM_024513.4	c.3945-6265G>C		intron_variant	Intron 14 of 17	ENST00000296137.7	NP_078789.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FYCO1	ENST00000296137.7	c.3945-6265G>C		intron_variant	Intron 14 of 17	1	NM_024513.4	ENSP00000296137.2
CXCR6	ENST00000438735.1	c.-22+1511C>G		intron_variant	Intron 1 of 1	3		ENSP00000396218.1
FYCO1	ENST00000433878.5	c.309-6265G>C		intron_variant	Intron 2 of 6	2		ENSP00000388136.1
FYCO1	ENST00000438446.1	c.-43-6265G>C		intron_variant	Intron 2 of 5	5		ENSP00000398517.1

Frequencies

GnomAD3 genomes AF: 0.787 AC: 119688 AN: 152126 Hom.: 47633 Cov.: 33

Gnomad AFR AF: 0.876

Gnomad AMI AF: 0.633

Gnomad AMR AF: 0.818

Gnomad ASJ AF: 0.783

Gnomad EAS AF: 0.959

Gnomad SAS AF: 0.870

Gnomad FIN AF: 0.759

Gnomad MID AF: 0.766

Gnomad NFE AF: 0.713

Gnomad OTH AF: 0.784

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

GnomAD4 genome AF: 0.787 AC: 119790 AN: 152246 Hom.: 47676 Cov.: 33 AF XY: 0.791 AC XY: 58866 AN XY: 74444

African (AFR) AF: 0.876 AC: 36403 AN: 41548

American (AMR) AF: 0.818 AC: 12515 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.783 AC: 2717 AN: 3470

East Asian (EAS) AF: 0.959 AC: 4968 AN: 5180

South Asian (SAS) AF: 0.870 AC: 4199 AN: 4826

European-Finnish (FIN) AF: 0.759 AC: 8052 AN: 10604

Middle Eastern (MID) AF: 0.779 AC: 229 AN: 294

European-Non Finnish (NFE) AF: 0.713 AC: 48466 AN: 67994

Other (OTH) AF: 0.787 AC: 1664 AN: 2114

Alfa AF: 0.646 Hom.: 1766

Bravo AF: 0.796

Asia WGS AF: 0.913 AC: 3172 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	1.6
DANN	Benign	0.42
PhyloP100		-0.090
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: rs2234350; hg19: chr3-45984300;