NM_001386809.1:c.719-63A>C

Variant names:

• chr17-4734715-T-G
• rs3744700
• NM_001386809.1:c.719-63A>C

Variant summary

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

The NM_001386809.1(CXCL16):​c.719-63A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.684 in 1,365,264 control chromosomes in the GnomAD database, including 323,322 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 0.66 (34000 hom., cov: 31)
  • Exomes 𝑓: 0.69 (289322 hom.)
• Consequence: CXCL16 NM_001386809.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.822
• Publications: 30 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 = 0.865 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001386809.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CXCL16	NM_001386809.1	MANE Select	c.719-63A>C		intron	N/A	NP_001373738.1	Q9H2A7
	CXCL16	NM_001100812.2		c.719-63A>C		intron	N/A	NP_001094282.2	Q9H2A7

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CXCL16	ENST00000293778.12	TSL:1 MANE Select	c.719-63A>C		intron	N/A	ENSP00000293778.7	Q9H2A7
	CXCL16	ENST00000574412.6	TSL:1	c.719-63A>C		intron	N/A	ENSP00000459592.2	Q9H2A7
	CXCL16	ENST00000886021.1		c.719-63A>C		intron	N/A	ENSP00000556080.1

Frequencies

GnomAD3 genomes AF: 0.664 AC: 100915 AN: 151894 Hom.: 33985 Cov.: 31

Gnomad AFR AF: 0.576

Gnomad AMI AF: 0.589

Gnomad AMR AF: 0.743

Gnomad ASJ AF: 0.673

Gnomad EAS AF: 0.886

Gnomad SAS AF: 0.882

Gnomad FIN AF: 0.748

Gnomad MID AF: 0.633

Gnomad NFE AF: 0.656

Gnomad OTH AF: 0.672

GnomAD4 exome AF: 0.687 AC: 833205 AN: 1213252 Hom.: 289322 AF XY: 0.693 AC XY: 426679 AN XY: 616090

African (AFR) AF: 0.574 AC: 16432 AN: 28650

American (AMR) AF: 0.829 AC: 36654 AN: 44216

Ashkenazi Jewish (ASJ) AF: 0.677 AC: 16590 AN: 24514

East Asian (EAS) AF: 0.869 AC: 33393 AN: 38440

South Asian (SAS) AF: 0.872 AC: 70609 AN: 80986

European-Finnish (FIN) AF: 0.736 AC: 38995 AN: 52988

Middle Eastern (MID) AF: 0.706 AC: 3728 AN: 5284

European-Non Finnish (NFE) AF: 0.656 AC: 581372 AN: 885938

Other (OTH) AF: 0.678 AC: 35432 AN: 52236

GnomAD4 genome AF: 0.664 AC: 100970 AN: 152012 Hom.: 34000 Cov.: 31 AF XY: 0.676 AC XY: 50239 AN XY: 74314

African (AFR) AF: 0.575 AC: 23836 AN: 41430

American (AMR) AF: 0.743 AC: 11352 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.673 AC: 2335 AN: 3472

East Asian (EAS) AF: 0.887 AC: 4584 AN: 5170

South Asian (SAS) AF: 0.882 AC: 4262 AN: 4832

European-Finnish (FIN) AF: 0.748 AC: 7904 AN: 10564

Middle Eastern (MID) AF: 0.609 AC: 179 AN: 294

European-Non Finnish (NFE) AF: 0.656 AC: 44565 AN: 67956

Other (OTH) AF: 0.671 AC: 1418 AN: 2112

Alfa AF: 0.666 Hom.: 67761

Bravo AF: 0.657

Asia WGS AF: 0.850 AC: 2955 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.7
DANN	Benign	0.71
PhyloP100		-0.82
Mutation Taster		=100/0	polymorphism (auto)

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: rs3744700; hg19: chr17-4638010;