rs4424334

Variant names:

• chr9-74321722-T-C
• rs4424334
• ENST00000715877.1:n.842+37923A>G

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+37923A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.539 in 152,008 control chromosomes in the GnomAD database, including 23,654 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 0.54 (23654 hom., cov: 32)
• Consequence: RORB-AS1 ENST00000715877.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.731
• Publications: 4 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=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.636 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
RORB-AS1	ENST00000715877.1	n.842+37923A>G		intron_variant	Intron 6 of 8

Frequencies

GnomAD3 genomes AF: 0.539 AC: 81891 AN: 151888 Hom.: 23667 Cov.: 32

Gnomad AFR AF: 0.316

Gnomad AMI AF: 0.593

Gnomad AMR AF: 0.585

Gnomad ASJ AF: 0.687

Gnomad EAS AF: 0.656

Gnomad SAS AF: 0.511

Gnomad FIN AF: 0.689

Gnomad MID AF: 0.640

Gnomad NFE AF: 0.625

Gnomad OTH AF: 0.584

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

GnomAD4 genome AF: 0.539 AC: 81879 AN: 152008 Hom.: 23654 Cov.: 32 AF XY: 0.542 AC XY: 40244 AN XY: 74264

African (AFR) AF: 0.315 AC: 13059 AN: 41450

American (AMR) AF: 0.584 AC: 8914 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.687 AC: 2383 AN: 3468

East Asian (EAS) AF: 0.655 AC: 3379 AN: 5160

South Asian (SAS) AF: 0.511 AC: 2461 AN: 4820

European-Finnish (FIN) AF: 0.689 AC: 7281 AN: 10566

Middle Eastern (MID) AF: 0.633 AC: 186 AN: 294

European-Non Finnish (NFE) AF: 0.625 AC: 42449 AN: 67970

Other (OTH) AF: 0.582 AC: 1227 AN: 2108

Alfa AF: 0.568 Hom.: 4003

Bravo AF: 0.524

Asia WGS AF: 0.540 AC: 1880 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.2
DANN	Benign	0.51
PhyloP100		-0.73

Splicing

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

Other links and lift over

dbSNP: rs4424334; hg19: chr9-76936638;