rs2814778
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
NM_002036 5_prime_UTR
Scores
2
Clinical Significance
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 |
---|---|---|---|---|---|---|---|
ACKR1 | NM_002036.4 | c.-67T>C | 5_prime_UTR_variant | 1/2 | ENST00000368122.4 | ||
ACKR1 | NM_001122951.3 | c.-111T>C | 5_prime_UTR_variant | 1/2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ACKR1 | ENST00000368122.4 | c.-67T>C | 5_prime_UTR_variant | 1/2 | 1 | NM_002036.4 | P2 | ||
ACKR1 | ENST00000368121.6 | c.-111T>C | 5_prime_UTR_variant | 1/2 | A2 | ||||
CADM3-AS1 | ENST00000609696.1 | n.164+2917A>G | intron_variant, non_coding_transcript_variant | 5 |
Frequencies
GnomAD3 genomes AF: 0.238 AC: 36137AN: 151932Hom.: 14312 Cov.: 31
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GnomAD4 exome AF: 0.0271 AC: 39396AN: 1453530Hom.: 13322 AF XY: 0.0240 AC XY: 17337AN XY: 723638
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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:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
Splicing
Find out SpliceAI and Pangolin per-transcript scores at