dbSNP rs863002: ACKR1:c.21+150C>T (chr1-159205130-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

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

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.15

Publications

21 publications found

Variant links:

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]

ACKR1 links:

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

CADM3-AS1 links:

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_002036.4. 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
	ACKR1	NM_002036.4	MANE Select	c.21+150C>T		intron	N/A	NP_002027.2
	ACKR1	NM_001122951.3		c.-24+150C>T		intron	N/A	NP_001116423.1	Q16570-2

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
ACKR1	ENST00000368122.4	TSL:1 MANE Select	c.21+150C>T	intron	N/A	ENSP00000357104.1	Q16570-1
ACKR1	ENST00000368121.6	TSL:6	c.-24+150C>T	intron	N/A	ENSP00000357103.2	Q16570-2
ACKR1	ENST00000851528.1		c.21+150C>T	intron	N/A	ENSP00000521587.1

Frequencies

GnomAD3 genomes

AF:

0.277

AC:

41934

AN:

151514

Hom.:

7393

Cov.:

show subpopulations

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.:

AF XY:

0.364

AC XY:

151154

AN XY:

415190

show subpopulations

African (AFR)

AF:

0.0586

AC:

1117

AN:

19056

American (AMR)

AF:

0.288

AC:

5831

AN:

20212

Ashkenazi Jewish (ASJ)

AF:

0.344

AC:

5536

AN:

16086

East Asian (EAS)

AF:

0.0816

AC:

2692

AN:

32994

South Asian (SAS)

AF:

0.338

AC:

17765

AN:

52508

European-Finnish (FIN)

AF:

0.401

AC:

17505

AN:

43704

Middle Eastern (MID)

AF:

0.272

AC:

1173

AN:

4314

European-Non Finnish (NFE)

AF:

0.396

AC:

236408

AN:

597600

Other (OTH)

AF:

0.340

AC:

12995

AN:

38176

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.509

Heterozygous variant carriers

9487

18974

28460

37947

47434

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

5794

11588

17382

23176

28970

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.276

AC:

41922

AN:

151634

Hom.:

7397

Cov.:

AF XY:

0.277

AC XY:

20546

AN XY:

74056

show subpopulations

African (AFR)

AF:

0.0676

AC:

2796

AN:

41334

American (AMR)

AF:

0.307

AC:

4682

AN:

15262

Ashkenazi Jewish (ASJ)

AF:

0.338

AC:

1173

AN:

3468

East Asian (EAS)

AF:

0.0614

AC:

316

AN:

5148

South Asian (SAS)

AF:

0.324

AC:

1554

AN:

4802

European-Finnish (FIN)

AF:

0.406

AC:

4231

AN:

10422

Middle Eastern (MID)

AF:

0.259

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.387

AC:

26294

AN:

67896

Other (OTH)

AF:

0.286

AC:

601

AN:

2102

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.509

Heterozygous variant carriers

1386

2772

4159

5545

6931

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

434

868

1302

1736

2170

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.331

Hom.:

19252

Bravo

AF:

0.256

Asia WGS

AF:

0.190

AC:

659

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.70

CADD

Benign

0.96

(source)

DANN

Benign

0.74

PhyloP100

-1.2

PromoterAI

0.014

Neutral

(source)

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over