rs6431472

Positions:

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

Variant summary

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

The XM_005246098.4(ACKR3):​c.-136+5045C>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: ACKR3 XM_005246098.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.381

Genes affected

ACKR3 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ACKR3	XM_005246098.4	c.-136+5045C>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

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

Gnomad4 AFR AF: 0.488

Gnomad4 AMR AF: 0.145

Gnomad4 ASJ AF: 0.131

Gnomad4 EAS AF: 0.168

Gnomad4 SAS AF: 0.162

Gnomad4 FIN AF: 0.0980

Gnomad4 NFE AF: 0.142

Gnomad4 OTH AF: 0.198

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 v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6431472; hg19: chr2-237451035;