chr1-159206153-G-A
Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2
The NM_002036.4(ACKR1):c.714G>A(p.Gly238=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00562 in 1,614,250 control chromosomes in the GnomAD database, including 39 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.0049 ( 3 hom., cov: 33)
Exomes 𝑓: 0.0057 ( 36 hom. )
Consequence
ACKR1
NM_002036.4 synonymous
NM_002036.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.687
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]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -11 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.85).
BP6
?
Variant 1-159206153-G-A is Benign according to our data. Variant chr1-159206153-G-A is described in ClinVar as [Benign]. Clinvar id is 777331.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=-0.687 with no splicing effect.
BS2
?
High Homozygotes in GnomAd at 3 BG gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ACKR1 | NM_002036.4 | c.714G>A | p.Gly238= | synonymous_variant | 2/2 | ENST00000368122.4 | |
ACKR1 | NM_001122951.3 | c.720G>A | p.Gly240= | synonymous_variant | 2/2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ACKR1 | ENST00000368122.4 | c.714G>A | p.Gly238= | synonymous_variant | 2/2 | 1 | NM_002036.4 | P2 | |
ACKR1 | ENST00000368121.6 | c.720G>A | p.Gly240= | synonymous_variant | 2/2 | A2 | |||
ACKR1 | ENST00000435307.2 | n.895G>A | non_coding_transcript_exon_variant | 1/1 | 3 | ||||
CADM3-AS1 | ENST00000609696.1 | n.164+1657C>T | intron_variant, non_coding_transcript_variant | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.00485 AC: 739AN: 152246Hom.: 3 Cov.: 33
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GnomAD3 exomes AF: 0.00535 AC: 1345AN: 251472Hom.: 8 AF XY: 0.00540 AC XY: 734AN XY: 135910
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GnomAD4 exome AF: 0.00570 AC: 8329AN: 1461886Hom.: 36 Cov.: 34 AF XY: 0.00577 AC XY: 4193AN XY: 727248
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GnomAD4 genome ? AF: 0.00486 AC: 740AN: 152364Hom.: 3 Cov.: 33 AF XY: 0.00466 AC XY: 347AN XY: 74508
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jul 31, 2018 | - - |
Computational scores
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Name
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BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at