rs7614670

Variant names:

• chr3-42879906-G-A
• rs7614670
• ENST00000426937.5:c.-163-28887G>A

Your query was ambiguous. Multiple possible variants found:

• chr3-42879906-G-A
• chr3-42879906-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000426937.5(ENSG00000290317):​c.-163-28887G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.367 in 152,082 control chromosomes in the GnomAD database, including 10,919 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 0.37 (10919 hom., cov: 32)
• Consequence: ENSG00000290317 ENST00000426937.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.252

Genes affected

ENSG00000290317 (HGNC:):

ACKR2 (HGNC:1565): (atypical chemokine receptor 2) This gene encodes a beta chemokine receptor, which is predicted to be a seven transmembrane protein similar to G protein-coupled receptors. Chemokines and their receptor-mediated signal transduction are critical for the recruitment of effector immune cells to the inflammation site. This gene is expressed in a range of tissues and hemopoietic cells. The expression of this receptor in lymphatic endothelial cells and overexpression in vascular tumors suggested its function in chemokine-driven recirculation of leukocytes and possible chemokine effects on the development and growth of vascular tumors. This receptor appears to bind the majority of beta-chemokine family members; however, its specific function remains unknown. This gene is mapped to chromosome 3p21.3, a region that includes a cluster of chemokine receptor genes. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.634 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000290317	ENST00000426937.5	c.-163-28887G>A		intron_variant	Intron 2 of 6	3		ENSP00000413859.1

Frequencies

GnomAD3 genomes AF: 0.367 AC: 55770 AN: 151962 Hom.: 10904 Cov.: 32

Gnomad AFR AF: 0.346

Gnomad AMI AF: 0.250

Gnomad AMR AF: 0.523

Gnomad ASJ AF: 0.301

Gnomad EAS AF: 0.652

Gnomad SAS AF: 0.460

Gnomad FIN AF: 0.315

Gnomad MID AF: 0.401

Gnomad NFE AF: 0.329

Gnomad OTH AF: 0.370

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.367 AC: 55826 AN: 152082 Hom.: 10919 Cov.: 32 AF XY: 0.372 AC XY: 27658 AN XY: 74340

Gnomad4 AFR AF: 0.346

Gnomad4 AMR AF: 0.524

Gnomad4 ASJ AF: 0.301

Gnomad4 EAS AF: 0.653

Gnomad4 SAS AF: 0.460

Gnomad4 FIN AF: 0.315

Gnomad4 NFE AF: 0.329

Gnomad4 OTH AF: 0.371

Alfa AF: 0.360 Hom.: 3865

Bravo AF: 0.386

Asia WGS AF: 0.519 AC: 1807 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.88
DANN	Benign	0.60

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

Other links and lift over

dbSNP: rs7614670; hg19: chr3-42921398;