rs863002

Positions:

• chr1-159205130-C-T

Variant summary

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

The NM_002036.4(ACKR1):​c.21+150C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.351 in 976,284 control chromosomes in the GnomAD database, including 66,004 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 0.28 (7397 hom., cov: 31)
  • Exomes 𝑓: 0.37 (58607 hom.)
• Consequence: ACKR1 NM_002036.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.15

Genes affected

ACKR1 (HGNC:4035): (atypical chemokine receptor 1 (Duffy blood group)) The protein encoded by this gene is a glycosylated membrane protein and a non-specific receptor for several chemokines. The encoded protein is the receptor for the human malarial parasites Plasmodium vivax and Plasmodium knowlesi. Polymorphisms in this gene are the basis of the Duffy blood group system. Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2008]

CADM3-AS1 (HGNC:40812): (CADM3 antisense RNA 1)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.7).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.383 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ACKR1	NM_002036.4	c.21+150C>T		intron_variant		ENST00000368122.4	NP_002027.2
ACKR1	NM_001122951.3	c.-24+150C>T		intron_variant			NP_001116423.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ACKR1	ENST00000368122.4	c.21+150C>T		intron_variant		1	NM_002036.4	ENSP00000357104.1
ACKR1	ENST00000368121.6	c.-24+150C>T		intron_variant		6		ENSP00000357103.2
CADM3-AS1	ENST00000609696.1	n.164+2680G>A		intron_variant		5

Frequencies

GnomAD3 genomes AF: 0.277 AC: 41934 AN: 151514 Hom.: 7393 Cov.: 31

Gnomad AFR AF: 0.0678

Gnomad AMI AF: 0.220

Gnomad AMR AF: 0.307

Gnomad ASJ AF: 0.338

Gnomad EAS AF: 0.0618

Gnomad SAS AF: 0.323

Gnomad FIN AF: 0.406

Gnomad MID AF: 0.266

Gnomad NFE AF: 0.387

Gnomad OTH AF: 0.289

GnomAD4 exome AF: 0.365 AC: 301022 AN: 824650 Hom.: 58607 Cov.: 11 AF XY: 0.364 AC XY: 151154 AN XY: 415190

Gnomad4 AFR exome AF: 0.0586

Gnomad4 AMR exome AF: 0.288

Gnomad4 ASJ exome AF: 0.344

Gnomad4 EAS exome AF: 0.0816

Gnomad4 SAS exome AF: 0.338

Gnomad4 FIN exome AF: 0.401

Gnomad4 NFE exome AF: 0.396

Gnomad4 OTH exome AF: 0.340

GnomAD4 genome AF: 0.276 AC: 41922 AN: 151634 Hom.: 7397 Cov.: 31 AF XY: 0.277 AC XY: 20546 AN XY: 74056

Gnomad4 AFR AF: 0.0676

Gnomad4 AMR AF: 0.307

Gnomad4 ASJ AF: 0.338

Gnomad4 EAS AF: 0.0614

Gnomad4 SAS AF: 0.324

Gnomad4 FIN AF: 0.406

Gnomad4 NFE AF: 0.387

Gnomad4 OTH AF: 0.286

Alfa AF: 0.362 Hom.: 13999

Bravo AF: 0.256

Asia WGS AF: 0.190 AC: 659 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.70
CADD	Benign	0.96
DANN	Benign	0.74

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: rs863002; hg19: chr1-159174920;