6-49606641-G-T
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Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_000324.3(RHAG):c.1212+207C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.48 in 483,398 control chromosomes in the GnomAD database, including 60,659 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.43 ( 16889 hom., cov: 31)
Exomes 𝑓: 0.50 ( 43770 hom. )
Consequence
RHAG
NM_000324.3 intron
NM_000324.3 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.321
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 -14 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.93).
BP6
?
Variant 6-49606641-G-T is Benign according to our data. Variant chr6-49606641-G-T is described in ClinVar as [Benign]. Clinvar id is 1221020.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
?
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.58 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RHAG | NM_000324.3 | c.1212+207C>A | intron_variant | ENST00000371175.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RHAG | ENST00000371175.10 | c.1212+207C>A | intron_variant | 1 | NM_000324.3 | P2 | |||
RHAG | ENST00000646272.1 | c.*29+88C>A | intron_variant | A2 | |||||
RHAG | ENST00000646939.1 | c.*34+207C>A | intron_variant | ||||||
RHAG | ENST00000646963.1 | c.1138+509C>A | intron_variant |
Frequencies
GnomAD3 genomes ? AF: 0.435 AC: 66053AN: 151794Hom.: 16888 Cov.: 31
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GnomAD4 exome AF: 0.501 AC: 166132AN: 331486Hom.: 43770 AF XY: 0.500 AC XY: 86248AN XY: 172452
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GnomAD4 genome ? AF: 0.435 AC: 66077AN: 151912Hom.: 16889 Cov.: 31 AF XY: 0.433 AC XY: 32111AN XY: 74216
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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 | GeneDx | Jun 19, 2021 | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at