Variant rs2814778 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 1P and 9B. PP5BP4BA1

The NM_002036.4(ACKR1):c.-67T>C variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0471 in 1,605,580 control chromosomes in the GnomAD database, including 27,684 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Pathogenic,association,protective (no stars).

Frequency

Genomes: 𝑓 0.24 ( 14362 hom., cov: 31)

Exomes 𝑓: 0.027 ( 13322 hom. )

Consequence

ACKR1
NM_002036.4 5_prime_UTR

Scores

Clinical Significance

Pathogenic; association; protective no assertion criteria provided P:1B:1O:1

Conservation

PhyloP100: 1.51

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:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -8 ACMG points.

PP5

Variant 1-159204893-T-C is Pathogenic according to our data. Variant chr1-159204893-T-C is described in ClinVar as [Pathogenic, association, protective]. Clinvar id is 18395.Status of the report is no_assertion_criteria_provided, 0 stars.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.33). . Strength limited to SUPPORTING due to the PP5.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.815 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ACKR1	NM_002036.4 linkuse as main transcript	c.-67T>C		5_prime_UTR_variant	1/2	ENST00000368122.4	NP_002027.2
ACKR1	NM_001122951.3 linkuse as main transcript	c.-111T>C		5_prime_UTR_variant	1/2		NP_001116423.1

Ensembl

Gene	Transcript	HGVSc	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ACKR1	ENST00000368122.4 linkuse as main transcript	c.-67T>C	5_prime_UTR_variant	1/2	1	NM_002036.4	ENSP00000357104	P2	Q16570-1
ACKR1	ENST00000368121.6 linkuse as main transcript	c.-111T>C	5_prime_UTR_variant	1/2			ENSP00000357103	A2	Q16570-2
CADM3-AS1	ENST00000609696.1 linkuse as main transcript	n.164+2917A>G	intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes

AF:

0.238

AC:

36137

AN:

151932

Hom.:

14312

Cov.:

show subpopulations

Gnomad AFR

AF:

0.822

Gnomad AMI

AF:

0.00110

Gnomad AMR

AF:

0.0903

Gnomad ASJ

AF:

0.0196

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.0104

Gnomad FIN

AF:

0.000471

Gnomad MID

AF:

0.171

Gnomad NFE

AF:

0.00373

Gnomad OTH

AF:

0.176

GnomAD4 exome

AF:

0.0271

AC:

39396

AN:

1453530

Hom.:

13322

Cov.:

AF XY:

0.0240

AC XY:

17337

AN XY:

723638

show subpopulations

Gnomad4 AFR exome

AF:

0.858

Gnomad4 AMR exome

AF:

0.0504

Gnomad4 ASJ exome

AF:

0.0227

Gnomad4 EAS exome

AF:

0.0000252

Gnomad4 SAS exome

AF:

0.00608

Gnomad4 FIN exome

AF:

0.000731

Gnomad4 NFE exome

AF:

0.00213

Gnomad4 OTH exome

AF:

0.0638

GnomAD4 genome

AF:

0.238

AC:

36236

AN:

152050

Hom.:

14362

Cov.:

AF XY:

0.230

AC XY:

17099

AN XY:

74310

show subpopulations

Gnomad4 AFR

AF:

0.822

Gnomad4 AMR

AF:

0.0901

Gnomad4 ASJ

AF:

0.0196

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00914

Gnomad4 FIN

AF:

0.000471

Gnomad4 NFE

AF:

0.00374

Gnomad4 OTH

AF:

0.174

Alfa

AF:

0.0519

Hom.:

3888

Asia WGS

AF:

0.0520

AC:

183

AN:

3478

ClinVar

Significance: Pathogenic; association; protective

Submissions summary: Pathogenic:1Benign:1Other:1

Revision: no assertion criteria provided

LINK: link

Submissions by phenotype

DUFFY BLOOD GROUP SYSTEM, FY(a-b-) PHENOTYPE

Pathogenic:1

Pathogenic, no assertion criteria provided

literature only

OMIM

Jan 01, 2010

- -

Resistance to Plasmodium vivax infection

Benign:1

protective, no assertion criteria provided

literature only

OMIM

Dec 11, 2017

- -

White blood cell count quantitative trait locus 1

Other:1

association, no assertion criteria provided

literature only

OMIM

Jan 01, 2010

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.33

CADD

Benign

DANN

Benign

0.94

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.16

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over