Variant rs2250333 details in Genebe, Genetics Data Aggregator

Variant summary

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

The ENST00000293778.12(CXCL16):c.218+8T>C variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.798 in 1,612,772 control chromosomes in the GnomAD database, including 517,122 homozygotes. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.74 ( 42191 hom., cov: 32)

Exomes 𝑓: 0.80 ( 474931 hom. )

Consequence

CXCL16
ENST00000293778.12 splice_region, intron

Scores

Splicing: ADA: 0.0001153

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.28

Variant links:

Genes affected

CXCL16 (HGNC:16642): (C-X-C motif chemokine ligand 16) Enables chemokine activity. Involved in several processes, including positive regulation of cell growth; response to interferon-gamma; and response to tumor necrosis factor. Located in extracellular space. Biomarker of COVID-19 and systemic scleroderma. [provided by Alliance of Genome Resources, Apr 2022]

CXCL16 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=-0.81).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.822 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CXCL16	NM_001386809.1 linkuse as main transcript	c.218+8T>C		splice_region_variant, intron_variant		ENST00000293778.12	NP_001373738.1
CXCL16	NM_001100812.2 linkuse as main transcript	c.218+8T>C		splice_region_variant, intron_variant			NP_001094282.2

Ensembl

Gene	Transcript	HGVSc	Effect	TSL	MANE	Protein	Appris
CXCL16	ENST00000293778.12 linkuse as main transcript	c.218+8T>C	splice_region_variant, intron_variant	1	NM_001386809.1	ENSP00000293778	P1
CXCL16	ENST00000574412.6 linkuse as main transcript	c.218+8T>C	splice_region_variant, intron_variant	1		ENSP00000459592	P1
CXCL16	ENST00000573123.1 linkuse as main transcript	c.56+8T>C	splice_region_variant, intron_variant	2		ENSP00000460145

Frequencies

GnomAD3 genomes

AF:

0.736

AC:

111881

AN:

152034

Hom.:

42148

Cov.:

show subpopulations

Gnomad AFR

AF:

0.562

Gnomad AMI

AF:

0.844

Gnomad AMR

AF:

0.775

Gnomad ASJ

AF:

0.841

Gnomad EAS

AF:

0.710

Gnomad SAS

AF:

0.670

Gnomad FIN

AF:

0.761

Gnomad MID

AF:

0.857

Gnomad NFE

AF:

0.827

Gnomad OTH

AF:

0.766

GnomAD3 exomes

AF:

0.762

AC:

190411

AN:

250032

Hom.:

73348

AF XY:

0.764

AC XY:

103365

AN XY:

135226

show subpopulations

Gnomad AFR exome

AF:

0.551

Gnomad AMR exome

AF:

0.723

Gnomad ASJ exome

AF:

0.849

Gnomad EAS exome

AF:

0.694

Gnomad SAS exome

AF:

0.691

Gnomad FIN exome

AF:

0.766

Gnomad NFE exome

AF:

0.823

Gnomad OTH exome

AF:

0.795

GnomAD4 exome

AF:

0.804

AC:

1174427

AN:

1460620

Hom.:

474931

Cov.:

AF XY:

0.802

AC XY:

582889

AN XY:

726584

show subpopulations

Gnomad4 AFR exome

AF:

0.560

Gnomad4 AMR exome

AF:

0.728

Gnomad4 ASJ exome

AF:

0.843

Gnomad4 EAS exome

AF:

0.708

Gnomad4 SAS exome

AF:

0.692

Gnomad4 FIN exome

AF:

0.764

Gnomad4 NFE exome

AF:

0.828

Gnomad4 OTH exome

AF:

0.792

GnomAD4 genome

AF:

0.736

AC:

111974

AN:

152152

Hom.:

42191

Cov.:

AF XY:

0.732

AC XY:

54443

AN XY:

74376

show subpopulations

Gnomad4 AFR

AF:

0.562

Gnomad4 AMR

AF:

0.775

Gnomad4 ASJ

AF:

0.841

Gnomad4 EAS

AF:

0.710

Gnomad4 SAS

AF:

0.671

Gnomad4 FIN

AF:

0.761

Gnomad4 NFE

AF:

0.828

Gnomad4 OTH

AF:

0.766

Alfa

AF:

0.807

Hom.:

116609

Bravo

AF:

0.730

Asia WGS

AF:

0.714

AC:

2484

AN:

3478

EpiCase

AF:

0.824

EpiControl

AF:

0.827

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.81

CADD

Benign

9.2

DANN

Benign

0.74

Splicing

Name

Calibrated prediction

Score

Prediction

dbscSNV1_ADA

Benign

0.00012

dbscSNV1_RF

Benign

0.0

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