rs7525133

Positions:

• chr1-156371703-G-A
• chr1-156371703-G-C
• chr1-156371703-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000537040.6(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 ENST00000537040.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.86

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]

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
RHBG	NM_020407.5	c.187+2267G>A		intron_variant		ENST00000537040.6	NP_065140.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
RHBG	ENST00000537040.6	c.187+2267G>A		intron_variant		1	NM_020407.5	ENSP00000441197	P1

Frequencies

GnomAD3 genomes AF: 0.0693 AC: 10536 AN: 152120 Hom.: 428 Cov.: 32

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: 65 AN: 906 Hom.: 1 Cov.: 0 AF XY: 0.0792 AC XY: 41 AN XY: 518

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.0968

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.0400

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.0727

Gnomad4 OTH exome AF: 0.0625

GnomAD4 genome AF: 0.0693 AC: 10551 AN: 152238 Hom.: 430 Cov.: 32 AF XY: 0.0663 AC XY: 4936 AN XY: 74430

Gnomad4 AFR AF: 0.0863

Gnomad4 AMR AF: 0.0572

Gnomad4 ASJ AF: 0.0648

Gnomad4 EAS AF: 0.0166

Gnomad4 SAS AF: 0.0404

Gnomad4 FIN AF: 0.0362

Gnomad4 NFE AF: 0.0733

Gnomad4 OTH AF: 0.0731

Alfa AF: 0.0695 Hom.: 856

Bravo AF: 0.0730

Asia WGS AF: 0.0410 AC: 145 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	12
DANN	Benign	0.45

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

Other links and lift over

dbSNP: rs7525133; hg19: chr1-156341494;