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GeneBe

17-4739388-C-T

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2

The NM_001386809.1(CXCL16):c.-49G>A variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00262 in 1,611,992 control chromosomes in the GnomAD database, including 69 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.012 ( 37 hom., cov: 31)
Exomes 𝑓: 0.0016 ( 32 hom. )

Consequence

CXCL16
NM_001386809.1 5_prime_UTR

Scores

2

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.287
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 -14 ACMG points.

BP4
?
    BP4 - Multiple lines of computational evidence suggest no impact on gene or gene product (conservation, evolutionary, splicing impact, etc.)
Computational evidence support a benign effect (BayesDel_noAF=-0.72).
BP6
?
    BP6 - Reputable source recently reports variant as benign, but the evidence is not available to the laboratory to perform an independent evaluation
Variant 17-4739388-C-T is Benign according to our data. Variant chr17-4739388-C-T is described in ClinVar as [Benign]. Clinvar id is 777097.Status of the report is criteria_provided_single_submitter, 1 stars.
BS1
?
    BS1 - Allele frequency is greater than expected for disorder
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.0121 (1842/152354) while in subpopulation AFR AF= 0.0396 (1647/41588). AF 95% confidence interval is 0.038. There are 37 homozygotes in gnomad4. There are 858 alleles in male gnomad4 subpopulation. Median coverage is 31. This position pass quality control queck.
BS2
?
    BS2 - Observed in a healthy adult individual for a recessive (homozygous), dominant (heterozygous), or X-linked (hemizygous) disorder, with full penetrance expected at an early age
High Homozygotes in GnomAd at 36 AR gene

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
CXCL16NM_001386809.1 linkuse as main transcriptc.-49G>A 5_prime_UTR_variant 1/6 ENST00000293778.12
CXCL16NM_001100812.2 linkuse as main transcriptc.-49G>A 5_prime_UTR_variant 1/5

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
CXCL16ENST00000293778.12 linkuse as main transcriptc.-49G>A 5_prime_UTR_variant 1/61 NM_001386809.1 P1
CXCL16ENST00000574412.6 linkuse as main transcriptc.-49G>A 5_prime_UTR_variant 1/51 P1

Frequencies

GnomAD3 genomes
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.0120
AC:
1834
AN:
152236
Hom.:
36
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.0395
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00929
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.000207
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00318
Gnomad NFE
AF:
0.000470
Gnomad OTH
AF:
0.00955
GnomAD3 exomes
AF:
0.00330
AC:
815
AN:
246778
Hom.:
8
AF XY:
0.00248
AC XY:
333
AN XY:
134264
show subpopulations
Gnomad AFR exome
AF:
0.0400
Gnomad AMR exome
AF:
0.00332
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.0000982
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.000442
Gnomad OTH exome
AF:
0.00298
GnomAD4 exome
AF:
0.00163
AC:
2386
AN:
1459638
Hom.:
32
Cov.:
32
AF XY:
0.00144
AC XY:
1046
AN XY:
726162
show subpopulations
Gnomad4 AFR exome
AF:
0.0418
Gnomad4 AMR exome
AF:
0.00424
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.0000580
Gnomad4 FIN exome
AF:
0.0000565
Gnomad4 NFE exome
AF:
0.000473
Gnomad4 OTH exome
AF:
0.00398
GnomAD4 genome
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.0121
AC:
1842
AN:
152354
Hom.:
37
Cov.:
31
AF XY:
0.0115
AC XY:
858
AN XY:
74494
show subpopulations
Gnomad4 AFR
AF:
0.0396
Gnomad4 AMR
AF:
0.00928
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.000207
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.000456
Gnomad4 OTH
AF:
0.00945
Alfa
AF:
0.00496
Hom.:
2
Bravo
AF:
0.0147
Asia WGS
AF:
0.00289
AC:
10
AN:
3478
EpiCase
AF:
0.000545
EpiControl
AF:
0.000474

ClinVar

Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not provided Benign:1
Benign, criteria provided, single submitterclinical testingInvitaeFeb 01, 2018- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.72
Cadd
Benign
7.9
Dann
Benign
0.80

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.

Other links and lift over

dbSNP: rs75334328; hg19: chr17-4642683; API