dbSNP rs7525133: RHBG:c.187+2267G>A (chr1-156371703-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_020407.5(RHBG):c.187+2267G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0693 in 153,144 control chromosomes in the GnomAD database, including 431 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.069 ( 430 hom., cov: 32)

Exomes 𝑓: 0.072 ( 1 hom. )

Consequence

RHBG
NM_020407.5 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.86

Publications

8 publications found

Variant links:

Genes affected

RHBG (HGNC:14572): (Rh family B glycoprotein) This gene encodes one of two non-erythroid members of the Rhesus (Rh) protein family. Non-erythroid Rh protein family members are mainly expressed in the kidney and belong to the methylammonium-ammonium permease/ammonia transporters superfamily. All Rh family proteins are predicted to be transmembrane proteins with 12 membrane spanning domains and intracytoplasmic N- and C-termini. Alternative splicing of this gene results in multiple transcript variants. [provided by RefSeq, Jan 2012]

RHBG links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.81).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0839 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_020407.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
RHBG	NM_020407.5	MANE Select	c.187+2267G>A	intron	N/A	NP_065140.3
RHBG	NR_146763.2		n.748G>A	non_coding_transcript_exon	Exon 2 of 12
RHBG	NM_001256396.2		c.97+449G>A	intron	N/A	NP_001243325.1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
RHBG	ENST00000537040.6	TSL:1 MANE Select	c.187+2267G>A	intron	N/A	ENSP00000441197.2
RHBG	ENST00000612897.4	TSL:1	n.260+449G>A	intron	N/A	ENSP00000477836.1
RHBG	ENST00000613460.4	TSL:1	n.187+2267G>A	intron	N/A	ENSP00000483178.1

Frequencies

GnomAD3 genomes

AF:

0.0693

AC:

10536

AN:

152120

Hom.:

428

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0862

Gnomad AMI

AF:

0.0548

Gnomad AMR

AF:

0.0573

Gnomad ASJ

AF:

0.0648

Gnomad EAS

AF:

0.0165

Gnomad SAS

AF:

0.0401

Gnomad FIN

AF:

0.0362

Gnomad MID

AF:

0.0443

Gnomad NFE

AF:

0.0733

Gnomad OTH

AF:

0.0734

GnomAD4 exome

AF:

0.0717

AC:

AN:

906

Hom.:

Cov.:

AF XY:

0.0792

AC XY:

AN XY:

518

show subpopulations

African (AFR)

AF:

0.00

AC:

AN:

American (AMR)

AF:

0.0968

AC:

AN:

124

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

East Asian (EAS)

AF:

0.00

AC:

AN:

South Asian (SAS)

AF:

0.0400

AC:

AN:

European-Finnish (FIN)

AF:

0.00

AC:

AN:

Middle Eastern (MID)

AF:

0.00

AC:

AN:

European-Non Finnish (NFE)

AF:

0.0727

AC:

AN:

674

Other (OTH)

AF:

0.0625

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.496

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.0693

AC:

10551

AN:

152238

Hom.:

430

Cov.:

AF XY:

0.0663

AC XY:

4936

AN XY:

74430

show subpopulations

African (AFR)

AF:

0.0863

AC:

3583

AN:

41534

American (AMR)

AF:

0.0572

AC:

874

AN:

15292

Ashkenazi Jewish (ASJ)

AF:

0.0648

AC:

225

AN:

3472

East Asian (EAS)

AF:

0.0166

AC:

AN:

5188

South Asian (SAS)

AF:

0.0404

AC:

195

AN:

4830

European-Finnish (FIN)

AF:

0.0362

AC:

384

AN:

10608

Middle Eastern (MID)

AF:

0.0476

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0733

AC:

4986

AN:

68002

Other (OTH)

AF:

0.0731

AC:

154

AN:

2106

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

503

1005

1508

2010

2513

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

128

256

384

512

640

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.0715

Hom.:

1796

Bravo

AF:

0.0730

Asia WGS

AF:

0.0410

AC:

145

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.81

CADD

Benign

(source)

DANN

Benign

0.45

PhyloP100

1.9

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

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

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over