rs6431472

Variant names:

• chr2-236542392-C-G
• rs6431472
• XM_005246098.4:c.-136+5045C>G

Your query was ambiguous. Multiple possible variants found:

• chr2-236542392-C-G
• chr2-236542392-C-T

Variant summary

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

The ENST00000780274.1(ENSG00000301621):​n.250+2239C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.235 in 152,092 control chromosomes in the GnomAD database, including 6,095 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 0.23 (6095 hom., cov: 32)
• Consequence: ENSG00000301621 ENST00000780274.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.381
• Publications: 5 publications found

Genes affected

ACKR3 (HGNC:23692): (atypical chemokine receptor 3) This gene encodes a member of the G-protein coupled receptor family. Although this protein was earlier thought to be a receptor for vasoactive intestinal peptide (VIP), it is now considered to be an orphan receptor, in that its endogenous ligand has not been identified. The protein is also a coreceptor for human immunodeficiency viruses (HIV). Translocations involving this gene and HMGA2 on chromosome 12 have been observed in lipomas. [provided by RefSeq, Jul 2008]

ACKR3 Gene-Disease associations (from GenCC):

• oculomotor-abducens synkinesis

  Inheritance: Unknown Classification: LIMITED Submitted by: Labcorp Genetics (formerly Invitae)

ENSG00000301621 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.482 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000780274.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000301621	ENST00000780274.1		n.250+2239C>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.235 AC: 35668 AN: 151974 Hom.: 6074 Cov.: 32

Gnomad AFR AF: 0.487

Gnomad AMI AF: 0.0252

Gnomad AMR AF: 0.145

Gnomad ASJ AF: 0.131

Gnomad EAS AF: 0.169

Gnomad SAS AF: 0.163

Gnomad FIN AF: 0.0980

Gnomad MID AF: 0.117

Gnomad NFE AF: 0.142

Gnomad OTH AF: 0.200

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

GnomAD4 genome AF: 0.235 AC: 35727 AN: 152092 Hom.: 6095 Cov.: 32 AF XY: 0.229 AC XY: 16995 AN XY: 74342

African (AFR) AF: 0.488 AC: 20217 AN: 41460

American (AMR) AF: 0.145 AC: 2216 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.131 AC: 453 AN: 3466

East Asian (EAS) AF: 0.168 AC: 870 AN: 5168

South Asian (SAS) AF: 0.162 AC: 780 AN: 4816

European-Finnish (FIN) AF: 0.0980 AC: 1038 AN: 10594

Middle Eastern (MID) AF: 0.112 AC: 33 AN: 294

European-Non Finnish (NFE) AF: 0.142 AC: 9679 AN: 67984

Other (OTH) AF: 0.198 AC: 418 AN: 2114

Alfa AF: 0.0870 Hom.: 115

Bravo AF: 0.250

Asia WGS AF: 0.182 AC: 630 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	2.0
DANN	Benign	0.34
PhyloP100		0.38

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs6431472;

hg19: chr2-237451035;