17-4739492-C-G

Variant names:

• chr17-4739492-C-G
• rs2304970
• NM_001386809.1:c.-153G>C

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_001386809.1(CXCL16):​c.-153G>C variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 34)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: CXCL16 NM_001386809.1 5_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.53
• Publications: 7 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: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CXCL16	NM_001386809.1	c.-153G>C		5_prime_UTR_variant	Exon 1 of 6	ENST00000293778.12	NP_001373738.1
CXCL16	NM_001100812.2	c.-153G>C		5_prime_UTR_variant	Exon 1 of 5		NP_001094282.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CXCL16	ENST00000293778.12	c.-153G>C		5_prime_UTR_variant	Exon 1 of 6	1	NM_001386809.1	ENSP00000293778.7
CXCL16	ENST00000574412.6	c.-153G>C		5_prime_UTR_variant	Exon 1 of 5	1		ENSP00000459592.2

Frequencies

GnomAD3 genomes Cov.: 34

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 975402 Hom.: 0 Cov.: 13 AF XY: 0.00 AC XY: 0 AN XY: 497984

African (AFR) AF: 0.00 AC: 0 AN: 22936

American (AMR) AF: 0.00 AC: 0 AN: 30578

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 21358

East Asian (EAS) AF: 0.00 AC: 0 AN: 34046

South Asian (SAS) AF: 0.00 AC: 0 AN: 70756

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 34896

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 3158

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 713820

Other (OTH) AF: 0.00 AC: 0 AN: 43854

GnomAD4 genome Cov.: 34

Alfa AF: 0.00 Hom.: 1888

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	1.2
DANN	Benign	0.49
PhyloP100		-1.5
PromoterAI		0.027	Neutral
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.0

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

Other links and lift over

dbSNP: rs2304970; hg19: chr17-4642787;