chr1-25290671-G-A
Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2
The NM_016124.6(RHD):c.366G>A(p.Ser122=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000326 in 1,378,290 control chromosomes in the GnomAD database, including 14 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.000046 ( 2 hom., cov: 20)
Exomes 𝑓: 0.000031 ( 12 hom. )
Consequence
RHD
NM_016124.6 synonymous
NM_016124.6 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -1.68
Genes affected
RHD (HGNC:10009): (Rh blood group D antigen) The Rh blood group system is the second most clinically significant of the blood groups, second only to ABO. It is also the most polymorphic of the blood groups, with variations due to deletions, gene conversions, and missense mutations. The Rh blood group includes this gene, which encodes the RhD protein, and a second gene that encodes both the RhC and RhE antigens on a single polypeptide. The two genes, and a third unrelated gene, are found in a cluster on chromosome 1. The classification of Rh-positive and Rh-negative individuals is determined by the presence or absence of the highly immunogenic RhD protein on the surface of erythrocytes. Multiple 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=-0.9).
BP6
?
Variant 1-25290671-G-A is Benign according to our data. Variant chr1-25290671-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 739638.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=-1.67 with no splicing effect.
BS2
?
High Homozygotes in GnomAd at 2 BG gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RHD | NM_016124.6 | c.366G>A | p.Ser122= | synonymous_variant | 3/10 | ENST00000328664.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RHD | ENST00000328664.9 | c.366G>A | p.Ser122= | synonymous_variant | 3/10 | 1 | NM_016124.6 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000459 AC: 6AN: 130736Hom.: 2 Cov.: 20
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GnomAD3 exomes AF: 0.0000533 AC: 12AN: 224982Hom.: 3 AF XY: 0.0000743 AC XY: 9AN XY: 121170
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GnomAD4 exome AF: 0.0000313 AC: 39AN: 1247436Hom.: 12 Cov.: 31 AF XY: 0.0000466 AC XY: 29AN XY: 622162
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GnomAD4 genome ? AF: 0.0000459 AC: 6AN: 130854Hom.: 2 Cov.: 20 AF XY: 0.0000469 AC XY: 3AN XY: 63940
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Apr 09, 2018 | - - |
Computational scores
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Name
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BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at