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rs2814778

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

2

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

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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 UniProt
ACKR1NM_002036.4 linkuse as main transcriptc.-67T>C 5_prime_UTR_variant 1/2 ENST00000368122.4
ACKR1NM_001122951.3 linkuse as main transcriptc.-111T>C 5_prime_UTR_variant 1/2

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
ACKR1ENST00000368122.4 linkuse as main transcriptc.-67T>C 5_prime_UTR_variant 1/21 NM_002036.4 P2Q16570-1
ACKR1ENST00000368121.6 linkuse as main transcriptc.-111T>C 5_prime_UTR_variant 1/2 A2Q16570-2
CADM3-AS1ENST00000609696.1 linkuse as main transcriptn.164+2917A>G intron_variant, non_coding_transcript_variant 5

Frequencies

GnomAD3 genomes
AF:
0.238
AC:
36137
AN:
151932
Hom.:
14312
Cov.:
31
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.:
29
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.:
31
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 providedliterature onlyOMIMJan 01, 2010- -
Resistance to Plasmodium vivax infection Benign:1
protective, no assertion criteria providedliterature onlyOMIMDec 11, 2017- -
White blood cell count quantitative trait locus 1 Other:1
association, no assertion criteria providedliterature onlyOMIMJan 01, 2010- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.33
Cadd
Benign
21
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.

Other links and lift over

dbSNP: rs2814778; hg19: chr1-159174683; API