rs2304970

Variant summary

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

The NM_001386809.1(CXCL16):​c.-153G>T variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.549 in 1,125,220 control chromosomes in the GnomAD database, including 171,660 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 0.56 ( 23637 hom., cov: 34)
Exomes 𝑓: 0.55 ( 148023 hom. )

Consequence

CXCL16
NM_001386809.1 5_prime_UTR

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.53
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]

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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=-0.77).
BA1
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.61 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
CXCL16NM_001386809.1 linkuse as main transcriptc.-153G>T 5_prime_UTR_variant 1/6 ENST00000293778.12
CXCL16NM_001100812.2 linkuse as main transcriptc.-153G>T 5_prime_UTR_variant 1/5

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
CXCL16ENST00000293778.12 linkuse as main transcriptc.-153G>T 5_prime_UTR_variant 1/61 NM_001386809.1 P1
CXCL16ENST00000574412.6 linkuse as main transcriptc.-153G>T 5_prime_UTR_variant 1/51 P1

Frequencies

GnomAD3 genomes
AF:
0.556
AC:
84551
AN:
151946
Hom.:
23612
Cov.:
34
show subpopulations
Gnomad AFR
AF:
0.557
Gnomad AMI
AF:
0.414
Gnomad AMR
AF:
0.621
Gnomad ASJ
AF:
0.619
Gnomad EAS
AF:
0.600
Gnomad SAS
AF:
0.589
Gnomad FIN
AF:
0.520
Gnomad MID
AF:
0.620
Gnomad NFE
AF:
0.539
Gnomad OTH
AF:
0.590
GnomAD4 exome
AF:
0.548
AC:
533334
AN:
973156
Hom.:
148023
Cov.:
13
AF XY:
0.551
AC XY:
273685
AN XY:
496866
show subpopulations
Gnomad4 AFR exome
AF:
0.557
Gnomad4 AMR exome
AF:
0.614
Gnomad4 ASJ exome
AF:
0.611
Gnomad4 EAS exome
AF:
0.578
Gnomad4 SAS exome
AF:
0.596
Gnomad4 FIN exome
AF:
0.525
Gnomad4 NFE exome
AF:
0.537
Gnomad4 OTH exome
AF:
0.558
GnomAD4 genome
AF:
0.557
AC:
84633
AN:
152064
Hom.:
23637
Cov.:
34
AF XY:
0.558
AC XY:
41507
AN XY:
74330
show subpopulations
Gnomad4 AFR
AF:
0.557
Gnomad4 AMR
AF:
0.621
Gnomad4 ASJ
AF:
0.619
Gnomad4 EAS
AF:
0.601
Gnomad4 SAS
AF:
0.590
Gnomad4 FIN
AF:
0.520
Gnomad4 NFE
AF:
0.539
Gnomad4 OTH
AF:
0.590
Alfa
AF:
0.467
Hom.:
1888
Bravo
AF:
0.564
Asia WGS
AF:
0.616
AC:
2144
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.77
CADD
Benign
3.3
DANN
Benign
0.74
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
1.0

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.010
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.

Other links and lift over

dbSNP: rs2304970; hg19: chr17-4642787; API