Variant 3-45947552-T-G details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_006564.2(CXCR6):c.*42T>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.522 in 1,499,736 control chromosomes in the GnomAD database, including 209,726 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 0.49 ( 19060 hom., cov: 33)

Exomes 𝑓: 0.53 ( 190666 hom. )

Consequence

CXCR6
NM_006564.2 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.152

Variant links:

Genes affected

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]

CXCR6 links:

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]

FYCO1 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.93).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.695 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CXCR6	NM_006564.2 linkuse as main transcript	c.*42T>G		3_prime_UTR_variant	2/2	ENST00000304552.5	NP_006555.1
FYCO1	NM_024513.4 linkuse as main transcript	c.3944+7697A>C		intron_variant		ENST00000296137.7	NP_078789.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CXCR6	ENST00000304552.5 linkuse as main transcript	c.*42T>G		3_prime_UTR_variant	2/2	1	NM_006564.2	ENSP00000304414	P1
FYCO1	ENST00000296137.7 linkuse as main transcript	c.3944+7697A>C		intron_variant		1	NM_024513.4	ENSP00000296137	P1	Q9BQS8-1

Frequencies

GnomAD3 genomes

AF:

0.486

AC:

73851

AN:

152000

Hom.:

19041

Cov.:

show subpopulations

Gnomad AFR

AF:

0.330

Gnomad AMI

AF:

0.584

Gnomad AMR

AF:

0.599

Gnomad ASJ

AF:

0.589

Gnomad EAS

AF:

0.665

Gnomad SAS

AF:

0.714

Gnomad FIN

AF:

0.581

Gnomad MID

AF:

0.532

Gnomad NFE

AF:

0.503

Gnomad OTH

AF:

0.497

GnomAD3 exomes

AF:

0.568

AC:

136644

AN:

240712

Hom.:

40058

AF XY:

0.571

AC XY:

74081

AN XY:

129760

show subpopulations

Gnomad AFR exome

AF:

0.327

Gnomad AMR exome

AF:

0.681

Gnomad ASJ exome

AF:

0.596

Gnomad EAS exome

AF:

0.662

Gnomad SAS exome

AF:

0.705

Gnomad FIN exome

AF:

0.585

Gnomad NFE exome

AF:

0.512

Gnomad OTH exome

AF:

0.558

GnomAD4 exome

AF:

0.527

AC:

709569

AN:

1347618

Hom.:

190666

Cov.:

AF XY:

0.532

AC XY:

358163

AN XY:

673448

show subpopulations

Gnomad4 AFR exome

AF:

0.329

Gnomad4 AMR exome

AF:

0.671

Gnomad4 ASJ exome

AF:

0.584

Gnomad4 EAS exome

AF:

0.625

Gnomad4 SAS exome

AF:

0.698

Gnomad4 FIN exome

AF:

0.574

Gnomad4 NFE exome

AF:

0.504

Gnomad4 OTH exome

AF:

0.544

GnomAD4 genome

AF:

0.486

AC:

73904

AN:

152118

Hom.:

19060

Cov.:

AF XY:

0.497

AC XY:

36959

AN XY:

74360

show subpopulations

Gnomad4 AFR

AF:

0.330

Gnomad4 AMR

AF:

0.599

Gnomad4 ASJ

AF:

0.589

Gnomad4 EAS

AF:

0.665

Gnomad4 SAS

AF:

0.715

Gnomad4 FIN

AF:

0.581

Gnomad4 NFE

AF:

0.503

Gnomad4 OTH

AF:

0.503

Alfa

AF:

0.510

Hom.:

40485

Bravo

AF:

0.473

Asia WGS

AF:

0.705

AC:

2450

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.93

CADD

Benign

4.4

DANN

Benign

0.42

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over