Genetic Variant RHBG:p.Asp425GlnfsTer26 (chr1-156384556-T-TCC) – ACMG Classification: Likely_benign (-4 pts)

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BS2

The NM_020407.5(RHBG):c.1270_1271dupCC(p.Asp425GlnfsTer26) variant causes a frameshift change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000814 in 1,584,358 control chromosomes in the GnomAD database, including 2 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.0015 ( 0 hom., cov: 0)

Exomes 𝑓: 0.00075 ( 2 hom. )

Consequence

RHBG
NM_020407.5 frameshift

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.618

Publications

17 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:

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ACMG classification

Classification was made for transcript

Our verdict: Likely_benign. The variant received -4 ACMG points.

BS2

High Homozygotes in GnomAdExome4 at 2 AR gene

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	HGVSp	Effect	Exon Rank	Protein
RHBG	NM_020407.5	MANE Select	c.1270_1271dupCC	p.Asp425GlnfsTer26	frameshift	Exon 9 of 10	NP_065140.3
RHBG	NM_001256396.2		c.1180_1181dupCC	p.Asp395GlnfsTer26	frameshift	Exon 10 of 11	NP_001243325.1
RHBG	NM_001256395.2		c.1063_1064dupCC	p.Asp356GlnfsTer26	frameshift	Exon 10 of 11	NP_001243324.1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein
RHBG	ENST00000537040.6	TSL:1 MANE Select	c.1270_1271dupCC	p.Asp425GlnfsTer26	frameshift	Exon 9 of 10	ENSP00000441197.2
RHBG	ENST00000612897.4	TSL:1	n.881_882dupCC		non_coding_transcript_exon	Exon 10 of 11	ENSP00000477836.1
RHBG	ENST00000613460.4	TSL:1	n.1099_1100dupCC		non_coding_transcript_exon	Exon 10 of 11	ENSP00000483178.1

Frequencies

GnomAD3 genomes

AF:

0.00146

AC:

221

AN:

151622

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00204

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00388

Gnomad ASJ

AF:

0.00576

Gnomad EAS

AF:

0.000194

Gnomad SAS

AF:

0.00229

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.0127

Gnomad NFE

AF:

0.000501

Gnomad OTH

AF:

0.00384

GnomAD4 exome

AF:

0.000746

AC:

1069

AN:

1432618

Hom.:

Cov.:

AF XY:

0.000768

AC XY:

546

AN XY:

710516

show subpopulations

African (AFR)

AF:

0.00232

AC:

AN:

32758

American (AMR)

AF:

0.00187

AC:

AN:

41778

Ashkenazi Jewish (ASJ)

AF:

0.00831

AC:

203

AN:

24420

East Asian (EAS)

AF:

0.000178

AC:

AN:

39284

South Asian (SAS)

AF:

0.00136

AC:

113

AN:

82958

European-Finnish (FIN)

AF:

0.000326

AC:

AN:

52132

Middle Eastern (MID)

AF:

0.0117

AC:

AN:

5622

European-Non Finnish (NFE)

AF:

0.000364

AC:

398

AN:

1094546

Other (OTH)

AF:

0.00188

AC:

111

AN:

59120

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.454

Heterozygous variant carriers

108

162

216

270

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Variant carriers

100

<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:

0.00146

AC:

221

AN:

151740

Hom.:

Cov.:

AF XY:

0.00159

AC XY:

118

AN XY:

74118

show subpopulations

African (AFR)

AF:

0.00206

AC:

AN:

41336

American (AMR)

AF:

0.00387

AC:

AN:

15240

Ashkenazi Jewish (ASJ)

AF:

0.00576

AC:

AN:

3470

East Asian (EAS)

AF:

0.000195

AC:

AN:

5130

South Asian (SAS)

AF:

0.00230

AC:

AN:

4790

European-Finnish (FIN)

AF:

0.00

AC:

AN:

10552

Middle Eastern (MID)

AF:

0.0136

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.000486

AC:

AN:

67912

Other (OTH)

AF:

0.00380

AC:

AN:

2106

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.495

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome 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

Alfa

AF:

0.00390

Hom.:

3475

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

PhyloP100

0.62

Mutation Taster

=107/93

polymorphism

(source)

Splicing

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

Publications

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1-156384556-TC-TCCC

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