Variant 1-156384556-T-TC details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1

The NM_020407.5(RHBG):c.1271dup(p.Asp425ArgfsTer18) variant causes a frameshift change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.711 in 1,584,428 control chromosomes in the GnomAD database, including 405,729 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.64 ( 32780 hom., cov: 0)

Exomes 𝑓: 0.72 ( 372949 hom. )

Consequence

RHBG
NM_020407.5 frameshift

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.618

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 made for transcript

Verdict is Benign. Variant got -8 ACMG points.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.734 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
RHBG	NM_020407.5 linkuse as main transcript	c.1271dup	p.Asp425ArgfsTer18	frameshift_variant	9/10	ENST00000537040.6	NP_065140.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
RHBG	ENST00000537040.6 linkuse as main transcript	c.1271dup	p.Asp425ArgfsTer18	frameshift_variant	9/10	1	NM_020407.5	ENSP00000441197	P1	Q9H310-1

Frequencies

GnomAD3 genomes

AF:

0.642

AC:

97260

AN:

151554

Hom.:

32771

Cov.:

show subpopulations

Gnomad AFR

AF:

0.438

Gnomad AMI

AF:

0.664

Gnomad AMR

AF:

0.707

Gnomad ASJ

AF:

0.733

Gnomad EAS

AF:

0.443

Gnomad SAS

AF:

0.665

Gnomad FIN

AF:

0.760

Gnomad MID

AF:

0.764

Gnomad NFE

AF:

0.740

Gnomad OTH

AF:

0.664

GnomAD4 exome

AF:

0.718

AC:

1029010

AN:

1432754

Hom.:

372949

Cov.:

AF XY:

0.717

AC XY:

509581

AN XY:

710592

show subpopulations

Gnomad4 AFR exome

AF:

0.421

Gnomad4 AMR exome

AF:

0.672

Gnomad4 ASJ exome

AF:

0.730

Gnomad4 EAS exome

AF:

0.466

Gnomad4 SAS exome

AF:

0.651

Gnomad4 FIN exome

AF:

0.746

Gnomad4 NFE exome

AF:

0.743

Gnomad4 OTH exome

AF:

0.696

GnomAD4 genome

AF:

0.642

AC:

97311

AN:

151674

Hom.:

32780

Cov.:

AF XY:

0.644

AC XY:

47707

AN XY:

74078

show subpopulations

Gnomad4 AFR

AF:

0.437

Gnomad4 AMR

AF:

0.708

Gnomad4 ASJ

AF:

0.733

Gnomad4 EAS

AF:

0.443

Gnomad4 SAS

AF:

0.665

Gnomad4 FIN

AF:

0.760

Gnomad4 NFE

AF:

0.740

Gnomad4 OTH

AF:

0.667

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

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

LitVar

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

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over