17-36104732-A-G

Variant names:

• chr17-36104732-A-G
• rs1719147
• NM_002984.4:c.191+90A>G

Variant summary

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

The NM_002984.4(CCL4):​c.191+90A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.767 in 1,535,036 control chromosomes in the GnomAD database, including 453,608 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 0.76 (44684 hom., cov: 31)
  • Exomes 𝑓: 0.77 (408924 hom.)
• Consequence: CCL4 NM_002984.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0820
• Publications: 15 publications found

Genes affected

CCL4 (HGNC:10630): (C-C motif chemokine ligand 4) The protein encoded by this gene is a mitogen-inducible monokine and is one of the major HIV-suppressive factors produced by CD8+ T-cells. The encoded protein is secreted and has chemokinetic and inflammatory functions. [provided by RefSeq, Dec 2012]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.913 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CCL4	NM_002984.4	c.191+90A>G		intron_variant	Intron 2 of 2	ENST00000615863.2	NP_002975.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CCL4	ENST00000615863.2	c.191+90A>G		intron_variant	Intron 2 of 2	1	NM_002984.4	ENSP00000482259.1
CCL4	ENST00000621626.1	c.77-493A>G		intron_variant	Intron 1 of 1	1		ENSP00000480569.1
CCL4	ENST00000613947.1	n.892A>G		non_coding_transcript_exon_variant	Exon 1 of 1	6

Frequencies

GnomAD3 genomes AF: 0.765 AC: 116182 AN: 151944 Hom.: 44641 Cov.: 31

Gnomad AFR AF: 0.722

Gnomad AMI AF: 0.807

Gnomad AMR AF: 0.838

Gnomad ASJ AF: 0.748

Gnomad EAS AF: 0.935

Gnomad SAS AF: 0.713

Gnomad FIN AF: 0.773

Gnomad MID AF: 0.766

Gnomad NFE AF: 0.763

Gnomad OTH AF: 0.777

GnomAD4 exome AF: 0.768 AC: 1061573 AN: 1382974 Hom.: 408924 Cov.: 22 AF XY: 0.765 AC XY: 526869 AN XY: 688822

African (AFR) AF: 0.726 AC: 23201 AN: 31942

American (AMR) AF: 0.879 AC: 35074 AN: 39916

Ashkenazi Jewish (ASJ) AF: 0.762 AC: 19210 AN: 25220

East Asian (EAS) AF: 0.950 AC: 36718 AN: 38648

South Asian (SAS) AF: 0.708 AC: 58574 AN: 82760

European-Finnish (FIN) AF: 0.765 AC: 39744 AN: 51952

Middle Eastern (MID) AF: 0.723 AC: 3851 AN: 5326

European-Non Finnish (NFE) AF: 0.763 AC: 801008 AN: 1049580

Other (OTH) AF: 0.767 AC: 44193 AN: 57630

GnomAD4 genome AF: 0.765 AC: 116282 AN: 152062 Hom.: 44684 Cov.: 31 AF XY: 0.765 AC XY: 56891 AN XY: 74340

African (AFR) AF: 0.722 AC: 29945 AN: 41454

American (AMR) AF: 0.839 AC: 12826 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.748 AC: 2596 AN: 3472

East Asian (EAS) AF: 0.935 AC: 4820 AN: 5156

South Asian (SAS) AF: 0.713 AC: 3437 AN: 4818

European-Finnish (FIN) AF: 0.773 AC: 8198 AN: 10600

Middle Eastern (MID) AF: 0.762 AC: 224 AN: 294

European-Non Finnish (NFE) AF: 0.763 AC: 51859 AN: 67954

Other (OTH) AF: 0.778 AC: 1641 AN: 2108

Alfa AF: 0.759 Hom.: 34691

Bravo AF: 0.772

Asia WGS AF: 0.847 AC: 2942 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	2.6
DANN	Benign	0.44
PhyloP100		0.082
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: rs1719147; hg19: chr17-34432125;