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GeneBe

6-49607181-G-A

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

Scores

1
9

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -1.17
Variant links:
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. This position pass quality control queck.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
RHAGNM_000324.3 linkuse as main transcriptc.1107C>T p.Ile369= synonymous_variant 8/10 ENST00000371175.10

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
RHAGENST00000371175.10 linkuse as main transcriptc.1107C>T p.Ile369= synonymous_variant 8/101 NM_000324.3 P2Q02094-1
RHAGENST00000646939.1 linkuse as main transcriptc.985C>T p.Arg329Trp missense_variant 7/9 Q02094-2
RHAGENST00000646272.1 linkuse as main transcriptc.1107C>T p.Ile369= synonymous_variant 8/10 A2
RHAGENST00000646963.1 linkuse as main transcriptc.1107C>T p.Ile369= synonymous_variant 8/9

Frequencies

GnomAD3 genomes
AF:
0.00108
AC:
164
AN:
152128
Hom.:
1
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.00381
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.000131
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.0000294
Gnomad OTH
AF:
0.000956
GnomAD3 exomes
AF:
0.000339
AC:
85
AN:
250486
Hom.:
0
AF XY:
0.000222
AC XY:
30
AN XY:
135330
show subpopulations
Gnomad AFR exome
AF:
0.00468
Gnomad AMR exome
AF:
0.000116
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.000109
Gnomad SAS exome
AF:
0.00
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.0000177
Gnomad OTH exome
AF:
0.000164
GnomAD4 exome
AF:
0.000115
AC:
168
AN:
1461390
Hom.:
0
Cov.:
30
AF XY:
0.0000963
AC XY:
70
AN XY:
726976
show subpopulations
Gnomad4 AFR exome
AF:
0.00403
Gnomad4 AMR exome
AF:
0.000134
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.000101
Gnomad4 SAS exome
AF:
0.0000464
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.00000450
Gnomad4 OTH exome
AF:
0.000232
GnomAD4 genome
AF:
0.00108
AC:
165
AN:
152244
Hom.:
1
Cov.:
33
AF XY:
0.000994
AC XY:
74
AN XY:
74418
show subpopulations
Gnomad4 AFR
AF:
0.00383
Gnomad4 AMR
AF:
0.000131
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.0000294
Gnomad4 OTH
AF:
0.000946
Alfa
AF:
0.000437
Hom.:
0
Bravo
AF:
0.00129
ESP6500AA
AF:
0.00522
AC:
23
ESP6500EA
AF:
0.000116
AC:
1
ExAC
AF:
0.000412
AC:
50
Asia WGS
AF:
0.000289
AC:
1
AN:
3478

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 submitterclinical testingInvitaeNov 13, 2023- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.56
Cadd
Benign
0.47
Dann
Uncertain
1.0
Eigen
Benign
-0.82
Eigen_PC
Benign
-0.86
FATHMM_MKL
Benign
0.023
N
LIST_S2
Benign
0.36
T
M_CAP
Benign
0.0032
T
MetaRNN
Benign
0.0065
T
MetaSVM
Benign
-0.92
T
MutationTaster
Benign
1.0
D;N
GERP RS
-5.1

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.020
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs141568382; hg19: chr6-49574894; API