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GeneBe

rs2814778

chr1-159204893-T-C

Variant summary

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

The NM_002036(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 0.238 in 151932 control chromosomes in the gnomAD Genomes database, including 14312 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 ( 14312 hom., cov: 31)

Consequence

ACKR1
NM_002036 5_prime_UTR

Scores

2

Clinical Significance

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

Conservation

PhyloP100: 1.51

Links

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
?
GnomAd 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
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
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
19
Dann
Benign
0.94

Splicing

Find out SpliceAI 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;