rs1051009

Variant names:

• chr17-4734591-G-A
• rs1051009
• NM_001386809.1:c.*15C>T

Your query was ambiguous. Multiple possible variants found:

• chr17-4734591-G-A
• chr17-4734591-G-C
• chr17-4734591-G-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001386809.1(CXCL16):​c.*15C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.337 in 1,594,374 control chromosomes in the GnomAD database, including 95,233 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 0.28 (7356 hom., cov: 32)
  • Exomes 𝑓: 0.34 (87877 hom.)
• Consequence: CXCL16 NM_001386809.1 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.238
• Publications: 32 publications found

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]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.492 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CXCL16	NM_001386809.1	c.*15C>T		3_prime_UTR_variant	Exon 5 of 6	ENST00000293778.12	NP_001373738.1
CXCL16	NM_001100812.2	c.*15C>T		3_prime_UTR_variant	Exon 5 of 5		NP_001094282.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CXCL16	ENST00000293778.12	c.*15C>T		3_prime_UTR_variant	Exon 5 of 6	1	NM_001386809.1	ENSP00000293778.7
CXCL16	ENST00000574412.6	c.*15C>T		3_prime_UTR_variant	Exon 5 of 5	1		ENSP00000459592.2
CXCL16	ENST00000575168.1	n.611C>T		non_coding_transcript_exon_variant	Exon 3 of 3	5
CXCL16	ENST00000576153.5	c.*15C>T		3_prime_UTR_variant	Exon 3 of 4	2		ENSP00000501470.1

Frequencies

GnomAD3 genomes AF: 0.280 AC: 42498 AN: 152010 Hom.: 7353 Cov.: 32

Gnomad AFR AF: 0.0680

Gnomad AMI AF: 0.257

Gnomad AMR AF: 0.395

Gnomad ASJ AF: 0.296

Gnomad EAS AF: 0.507

Gnomad SAS AF: 0.361

Gnomad FIN AF: 0.349

Gnomad MID AF: 0.291

Gnomad NFE AF: 0.348

Gnomad OTH AF: 0.297

GnomAD2 exomes AF: 0.352 AC: 88372 AN: 251412 AF XY: 0.351

Gnomad AFR exome AF: 0.0630

Gnomad AMR exome AF: 0.448

Gnomad ASJ exome AF: 0.299

Gnomad EAS exome AF: 0.503

Gnomad FIN exome AF: 0.345

Gnomad NFE exome AF: 0.343

Gnomad OTH exome AF: 0.343

GnomAD4 exome AF: 0.343 AC: 494138 AN: 1442246 Hom.: 87877 Cov.: 28 AF XY: 0.344 AC XY: 247018 AN XY: 718708

African (AFR) AF: 0.0532 AC: 1772 AN: 33280

American (AMR) AF: 0.440 AC: 19657 AN: 44634

Ashkenazi Jewish (ASJ) AF: 0.296 AC: 7681 AN: 25972

East Asian (EAS) AF: 0.496 AC: 19606 AN: 39548

South Asian (SAS) AF: 0.361 AC: 31000 AN: 85870

European-Finnish (FIN) AF: 0.345 AC: 18382 AN: 53306

Middle Eastern (MID) AF: 0.256 AC: 1464 AN: 5718

European-Non Finnish (NFE) AF: 0.343 AC: 375117 AN: 1094236

Other (OTH) AF: 0.326 AC: 19459 AN: 59682

GnomAD4 genome AF: 0.279 AC: 42506 AN: 152128 Hom.: 7356 Cov.: 32 AF XY: 0.285 AC XY: 21180 AN XY: 74352

African (AFR) AF: 0.0679 AC: 2818 AN: 41522

American (AMR) AF: 0.395 AC: 6043 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.296 AC: 1028 AN: 3472

East Asian (EAS) AF: 0.508 AC: 2624 AN: 5166

South Asian (SAS) AF: 0.360 AC: 1737 AN: 4822

European-Finnish (FIN) AF: 0.349 AC: 3679 AN: 10550

Middle Eastern (MID) AF: 0.276 AC: 81 AN: 294

European-Non Finnish (NFE) AF: 0.348 AC: 23633 AN: 67982

Other (OTH) AF: 0.298 AC: 629 AN: 2112

Alfa AF: 0.325 Hom.: 14679

Bravo AF: 0.274

Asia WGS AF: 0.428 AC: 1489 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	4.2
DANN	Benign	0.49
PhyloP100		0.24
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.030		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs1051009; hg19: chr17-4637886; COSMIC: COSV53411277; COSMIC: COSV53411277;