rs10491923

Variant names:

• chr9-74334264-C-T
• rs10491923
• ENST00000715877.1:n.842+25381G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000715877.1(RORB-AS1):​n.842+25381G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.22 in 152,034 control chromosomes in the GnomAD database, including 4,297 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 0.22 (4297 hom., cov: 32)
• Consequence: RORB-AS1 ENST00000715877.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.387
• Publications: 1 publications found

Genes affected

RORB-AS1 (HGNC:49803): (RORB antisense RNA 1)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.283 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000715877.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	RORB-AS1	ENST00000715877.1		n.842+25381G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.220 AC: 33384 AN: 151916 Hom.: 4281 Cov.: 32

Gnomad AFR AF: 0.0873

Gnomad AMI AF: 0.205

Gnomad AMR AF: 0.279

Gnomad ASJ AF: 0.203

Gnomad EAS AF: 0.295

Gnomad SAS AF: 0.282

Gnomad FIN AF: 0.246

Gnomad MID AF: 0.115

Gnomad NFE AF: 0.274

Gnomad OTH AF: 0.228

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

GnomAD4 genome AF: 0.220 AC: 33442 AN: 152034 Hom.: 4297 Cov.: 32 AF XY: 0.222 AC XY: 16454 AN XY: 74284

African (AFR) AF: 0.0878 AC: 3645 AN: 41500

American (AMR) AF: 0.279 AC: 4256 AN: 15230

Ashkenazi Jewish (ASJ) AF: 0.203 AC: 702 AN: 3464

East Asian (EAS) AF: 0.295 AC: 1527 AN: 5172

South Asian (SAS) AF: 0.282 AC: 1361 AN: 4834

European-Finnish (FIN) AF: 0.246 AC: 2592 AN: 10556

Middle Eastern (MID) AF: 0.120 AC: 35 AN: 292

European-Non Finnish (NFE) AF: 0.274 AC: 18649 AN: 67964

Other (OTH) AF: 0.231 AC: 488 AN: 2110

Alfa AF: 0.254 Hom.: 15692

Bravo AF: 0.215

Asia WGS AF: 0.299 AC: 1039 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	3.9
DANN	Benign	0.20
PhyloP100		0.39

Splicing

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

Other links and lift over

dbSNP: rs10491923; hg19: chr9-76949180;