Variant 17-4738460-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1

The ENST00000293778.12(CXCL16):c.249G>A(p.Gly83=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.744 in 1,612,134 control chromosomes in the GnomAD database, including 450,643 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 0.67 ( 35504 hom., cov: 32)

Exomes 𝑓: 0.75 ( 415139 hom. )

Consequence

CXCL16
ENST00000293778.12 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.669

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 -13 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.69).

BP7

Synonymous conserved (PhyloP=-0.669 with no splicing effect.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.767 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.249G>A	p.Gly83=	synonymous_variant	3/6	ENST00000293778.12	NP_001373738.1
CXCL16	NM_001100812.2 linkuse as main transcript	c.249G>A	p.Gly83=	synonymous_variant	3/5		NP_001094282.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris
CXCL16	ENST00000293778.12 linkuse as main transcript	c.249G>A	p.Gly83=	synonymous_variant	3/6	1	NM_001386809.1	ENSP00000293778	P1
CXCL16	ENST00000574412.6 linkuse as main transcript	c.249G>A	p.Gly83=	synonymous_variant	3/5	1		ENSP00000459592	P1
CXCL16	ENST00000573123.1 linkuse as main transcript	c.87G>A	p.Gly29=	synonymous_variant	2/3	2		ENSP00000460145
CXCL16	ENST00000575168.1 linkuse as main transcript	n.80G>A		non_coding_transcript_exon_variant	1/3	5

Frequencies

GnomAD3 genomes

AF:

0.670

AC:

101752

AN:

151978

Hom.:

35479

Cov.:

show subpopulations

Gnomad AFR

AF:

0.453

Gnomad AMI

AF:

0.730

Gnomad AMR

AF:

0.725

Gnomad ASJ

AF:

0.778

Gnomad EAS

AF:

0.707

Gnomad SAS

AF:

0.656

Gnomad FIN

AF:

0.710

Gnomad MID

AF:

0.794

Gnomad NFE

AF:

0.773

Gnomad OTH

AF:

0.709

GnomAD3 exomes

AF:

0.715

AC:

179152

AN:

250528

Hom.:

64917

AF XY:

0.720

AC XY:

97536

AN XY:

135408

show subpopulations

Gnomad AFR exome

AF:

0.442

Gnomad AMR exome

AF:

0.689

Gnomad ASJ exome

AF:

0.782

Gnomad EAS exome

AF:

0.692

Gnomad SAS exome

AF:

0.678

Gnomad FIN exome

AF:

0.715

Gnomad NFE exome

AF:

0.768

Gnomad OTH exome

AF:

0.745

GnomAD4 exome

AF:

0.752

AC:

1097333

AN:

1460038

Hom.:

415139

Cov.:

AF XY:

0.751

AC XY:

545476

AN XY:

726362

show subpopulations

Gnomad4 AFR exome

AF:

0.446

Gnomad4 AMR exome

AF:

0.694

Gnomad4 ASJ exome

AF:

0.778

Gnomad4 EAS exome

AF:

0.707

Gnomad4 SAS exome

AF:

0.679

Gnomad4 FIN exome

AF:

0.714

Gnomad4 NFE exome

AF:

0.772

Gnomad4 OTH exome

AF:

0.739

GnomAD4 genome

AF:

0.669

AC:

101814

AN:

152096

Hom.:

35504

Cov.:

AF XY:

0.667

AC XY:

49550

AN XY:

74320

show subpopulations

Gnomad4 AFR

AF:

0.453

Gnomad4 AMR

AF:

0.725

Gnomad4 ASJ

AF:

0.778

Gnomad4 EAS

AF:

0.708

Gnomad4 SAS

AF:

0.656

Gnomad4 FIN

AF:

0.710

Gnomad4 NFE

AF:

0.773

Gnomad4 OTH

AF:

0.709

Alfa

AF:

0.724

Hom.:

28799

Bravo

AF:

0.661

Asia WGS

AF:

0.695

AC:

2419

AN:

3478

EpiCase

AF:

0.771

EpiControl

AF:

0.776

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.69

CADD

Benign

5.7

DANN

Benign

0.74

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.7

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