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

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BS2

The NM_020407.5(RHBG):c.1270_1271dup(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

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 Likely_benign. Variant got -4 ACMG points.

BS2

High Homozygotes in GnomAdExome4 at 2 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
RHBG	NM_020407.5 linkuse as main transcript	c.1270_1271dup	p.Asp425GlnfsTer26	frameshift_variant	9/10	ENST00000537040.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
RHBG	ENST00000537040.6 linkuse as main transcript	c.1270_1271dup	p.Asp425GlnfsTer26	frameshift_variant	9/10	1	NM_020407.5	P1	Q9H310-1

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

Gnomad4 AFR exome

AF:

0.00232

Gnomad4 AMR exome

AF:

0.00187

Gnomad4 ASJ exome

AF:

0.00831

Gnomad4 EAS exome

AF:

0.000178

Gnomad4 SAS exome

AF:

0.00136

Gnomad4 FIN exome

AF:

0.000326

Gnomad4 NFE exome

AF:

0.000364

Gnomad4 OTH exome

AF:

0.00188

GnomAD4 genome

AF:

0.00146

AC:

221

AN:

151740

Hom.:

Cov.:

AF XY:

0.00159

AC XY:

118

AN XY:

74118

show subpopulations

Gnomad4 AFR

AF:

0.00206

Gnomad4 AMR

AF:

0.00387

Gnomad4 ASJ

AF:

0.00576

Gnomad4 EAS

AF:

0.000195

Gnomad4 SAS

AF:

0.00230

Gnomad4 FIN

AF:

0.00

Gnomad4 NFE

AF:

0.000486

Gnomad4 OTH

AF:

0.00380

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

Splicing

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