rs6752707

chr2-226902106-C-G

Variant summary

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

The NM_001167608.3(RHBDD1):c.567-4687C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.436 in 151,996 control chromosomes in the GnomAD database, including 14,616 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 0.44 (14616 hom., cov: 32)
• Consequence: RHBDD1 NM_001167608.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.391

Genes affected

RHBDD1 (HGNC:23081): (rhomboid domain containing 1) Enables serine-type endopeptidase activity. Involved in several processes, including cellular response to unfolded protein; membrane protein proteolysis; and positive regulation of protein catabolic process. Located in endoplasmic reticulum. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.486 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
RHBDD1	NM_001167608.3	c.567-4687C>G		intron_variant		ENST00000392062.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
RHBDD1	ENST00000392062.7	c.567-4687C>G		intron_variant		5	NM_001167608.3	P1
RHBDD1	ENST00000341329.7	c.567-4687C>G		intron_variant		1		P1

Frequencies

GnomAD3 genomes AF: 0.436 AC: 66144 AN: 151876 Hom.: 14586 Cov.: 32

Gnomad AFR AF: 0.491

Gnomad AMI AF: 0.381

Gnomad AMR AF: 0.443

Gnomad ASJ AF: 0.400

Gnomad EAS AF: 0.352

Gnomad SAS AF: 0.502

Gnomad FIN AF: 0.473

Gnomad MID AF: 0.328

Gnomad NFE AF: 0.400

Gnomad OTH AF: 0.395

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.436 AC: 66224 AN: 151996 Hom.: 14616 Cov.: 32 AF XY: 0.438 AC XY: 32534 AN XY: 74298

Gnomad4 AFR AF: 0.492

Gnomad4 AMR AF: 0.444

Gnomad4 ASJ AF: 0.400

Gnomad4 EAS AF: 0.353

Gnomad4 SAS AF: 0.501

Gnomad4 FIN AF: 0.473

Gnomad4 NFE AF: 0.400

Gnomad4 OTH AF: 0.390

Alfa AF: 0.428 Hom.: 1710

Bravo AF: 0.436

Asia WGS AF: 0.442 AC: 1539 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
Cadd	Benign	2.4
Dann	Benign	0.71

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: rs6752707; hg19: chr2-227766822;