rs13417106

Positions:

• chr2-226819112-A-G

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The NM_001349069.2(RHBDD1):​c.-91+10475A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.242 in 152,066 control chromosomes in the GnomAD database, including 8,348 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 0.24 (8348 hom., cov: 30)
• Consequence: RHBDD1 NM_001349069.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.562

Genes affected

RHBDD1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.33).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.597 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
RHBDD1	NM_001349069.2	c.-91+10475A>G		intron_variant			NP_001335998.1
RHBDD1	XM_047445998.1	c.-91+10475A>G		intron_variant			XP_047301954.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.241 AC: 36637 AN: 151950 Hom.: 8310 Cov.: 30

Gnomad AFR AF: 0.603

Gnomad AMI AF: 0.115

Gnomad AMR AF: 0.165

Gnomad ASJ AF: 0.0455

Gnomad EAS AF: 0.161

Gnomad SAS AF: 0.146

Gnomad FIN AF: 0.0886

Gnomad MID AF: 0.0791

Gnomad NFE AF: 0.0887

Gnomad OTH AF: 0.192

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

GnomAD4 genome AF: 0.242 AC: 36735 AN: 152066 Hom.: 8348 Cov.: 30 AF XY: 0.237 AC XY: 17622 AN XY: 74358

Gnomad4 AFR AF: 0.604

Gnomad4 AMR AF: 0.165

Gnomad4 ASJ AF: 0.0455

Gnomad4 EAS AF: 0.161

Gnomad4 SAS AF: 0.146

Gnomad4 FIN AF: 0.0886

Gnomad4 NFE AF: 0.0887

Gnomad4 OTH AF: 0.191

Alfa AF: 0.193 Hom.: 711

Bravo AF: 0.263

Asia WGS AF: 0.197 AC: 686 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.33
CADD	Benign	18
DANN	Benign	0.67

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13417106; hg19: chr2-227683828;