9-74302924-C-T

Variant names:

• chr9-74302924-C-T
• rs10746953
• ENST00000715877.1:n.843-20960G>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.843-20960G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.443 in 151,784 control chromosomes in the GnomAD database, including 16,424 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 (16424 hom., cov: 31)
• Consequence: RORB-AS1 ENST00000715877.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.708
• Publications: 8 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=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.719 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

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

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	RORB-AS1	ENST00000715877.1		n.843-20960G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.443 AC: 67193 AN: 151666 Hom.: 16428 Cov.: 31

Gnomad AFR AF: 0.239

Gnomad AMI AF: 0.458

Gnomad AMR AF: 0.514

Gnomad ASJ AF: 0.445

Gnomad EAS AF: 0.739

Gnomad SAS AF: 0.504

Gnomad FIN AF: 0.604

Gnomad MID AF: 0.380

Gnomad NFE AF: 0.500

Gnomad OTH AF: 0.443

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

GnomAD4 genome AF: 0.443 AC: 67192 AN: 151784 Hom.: 16424 Cov.: 31 AF XY: 0.451 AC XY: 33411 AN XY: 74160

African (AFR) AF: 0.238 AC: 9859 AN: 41396

American (AMR) AF: 0.513 AC: 7834 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.445 AC: 1545 AN: 3470

East Asian (EAS) AF: 0.739 AC: 3800 AN: 5142

South Asian (SAS) AF: 0.503 AC: 2416 AN: 4804

European-Finnish (FIN) AF: 0.604 AC: 6345 AN: 10504

Middle Eastern (MID) AF: 0.388 AC: 114 AN: 294

European-Non Finnish (NFE) AF: 0.500 AC: 33930 AN: 67894

Other (OTH) AF: 0.443 AC: 932 AN: 2102

Alfa AF: 0.478 Hom.: 27749

Bravo AF: 0.431

Asia WGS AF: 0.550 AC: 1912 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.0
DANN	Benign	0.57
PhyloP100		-0.71

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs10746953;

hg19: chr9-76917840;

COSMIC: COSV107153597;