6-49607181-G-A
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Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS1
The NM_000324.3(RHAG):c.1107C>T(p.Ile369=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000206 in 1,613,634 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.0011 ( 1 hom., cov: 33)
Exomes 𝑓: 0.00011 ( 0 hom. )
Consequence
RHAG
NM_000324.3 synonymous
NM_000324.3 synonymous
Scores
1
9
Clinical Significance
Conservation
PhyloP100: -1.17
Genes affected
RHAG (HGNC:10006): (Rh associated glycoprotein) The protein encoded by this gene is erythrocyte-specific and is thought to be part of a membrane channel that transports ammonium and carbon dioxide across the blood cell membrane. The encoded protein appears to interact with Rh blood group antigens and Rh30 polypeptides. Defects in this gene are a cause of regulator type Rh-null hemolytic anemia (RHN), or Rh-deficiency syndrome.[provided by RefSeq, Mar 2009]
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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 (MetaRNN=0.006500989).
BP6
?
Variant 6-49607181-G-A is Benign according to our data. Variant chr6-49607181-G-A is described in ClinVar as [Benign]. Clinvar id is 2712934.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=-1.17 with no splicing effect.
BS1
?
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.00108 (165/152244) while in subpopulation AFR AF= 0.00383 (159/41552). AF 95% confidence interval is 0.00334. There are 1 homozygotes in gnomad4. There are 74 alleles in male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RHAG | NM_000324.3 | c.1107C>T | p.Ile369= | synonymous_variant | 8/10 | ENST00000371175.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RHAG | ENST00000371175.10 | c.1107C>T | p.Ile369= | synonymous_variant | 8/10 | 1 | NM_000324.3 | P2 | |
RHAG | ENST00000646939.1 | c.985C>T | p.Arg329Trp | missense_variant | 7/9 | ||||
RHAG | ENST00000646272.1 | c.1107C>T | p.Ile369= | synonymous_variant | 8/10 | A2 | |||
RHAG | ENST00000646963.1 | c.1107C>T | p.Ile369= | synonymous_variant | 8/9 |
Frequencies
GnomAD3 genomes ? AF: 0.00108 AC: 164AN: 152128Hom.: 1 Cov.: 33
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GnomAD3 exomes AF: 0.000339 AC: 85AN: 250486Hom.: 0 AF XY: 0.000222 AC XY: 30AN XY: 135330
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GnomAD4 exome AF: 0.000115 AC: 168AN: 1461390Hom.: 0 Cov.: 30 AF XY: 0.0000963 AC XY: 70AN XY: 726976
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GnomAD4 genome ? AF: 0.00108 AC: 165AN: 152244Hom.: 1 Cov.: 33 AF XY: 0.000994 AC XY: 74AN XY: 74418
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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 | Nov 13, 2023 | - - |
Computational scores
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Name
Calibrated prediction
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BayesDel_noAF
Benign
CADD
Benign
DANN
Uncertain
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Benign
Eigen_PC
Benign
FATHMM_MKL
Benign
N
LIST_S2
Benign
T
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Benign
T
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Benign
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MetaSVM
Benign
T
MutationTaster
Benign
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at