XR_242624.4:n.686-2600C>G

Variant names:

• chr9-74126500-G-C
• rs4237260
• ENST00000715876.1:n.858-2600C>G

Variant summary

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

The XR_242624.4(LOC101927329):​n.686-2600C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.206 in 152,034 control chromosomes in the GnomAD database, including 3,964 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 0.21 (3964 hom., cov: 32)
• Consequence: LOC101927329 XR_242624.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.106
• Publications: 2 publications found

Genes affected

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

LOC101927329 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.444 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000715876.1. 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	ENST00000715876.1		n.858-2600C>G		intron	N/A
	RORB-AS1	ENST00000722221.1		n.687-2600C>G		intron	N/A
	RORB-AS1	ENST00000722222.1		n.955-2600C>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.207 AC: 31387 AN: 151916 Hom.: 3970 Cov.: 32

Gnomad AFR AF: 0.0750

Gnomad AMI AF: 0.340

Gnomad AMR AF: 0.318

Gnomad ASJ AF: 0.312

Gnomad EAS AF: 0.459

Gnomad SAS AF: 0.347

Gnomad FIN AF: 0.170

Gnomad MID AF: 0.225

Gnomad NFE AF: 0.230

Gnomad OTH AF: 0.239

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

GnomAD4 genome AF: 0.206 AC: 31381 AN: 152034 Hom.: 3964 Cov.: 32 AF XY: 0.210 AC XY: 15603 AN XY: 74290

African (AFR) AF: 0.0750 AC: 3111 AN: 41482

American (AMR) AF: 0.318 AC: 4851 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.312 AC: 1081 AN: 3466

East Asian (EAS) AF: 0.459 AC: 2371 AN: 5164

South Asian (SAS) AF: 0.347 AC: 1669 AN: 4814

European-Finnish (FIN) AF: 0.170 AC: 1790 AN: 10538

Middle Eastern (MID) AF: 0.221 AC: 65 AN: 294

European-Non Finnish (NFE) AF: 0.230 AC: 15636 AN: 67976

Other (OTH) AF: 0.236 AC: 498 AN: 2114

Alfa AF: 0.209 Hom.: 473

Bravo AF: 0.213

Asia WGS AF: 0.349 AC: 1213 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	1.7
DANN	Benign	0.51
PhyloP100		0.11

Splicing

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

Other links and lift over

dbSNP: rs4237260; hg19: chr9-76741416; COSMIC: COSV60360500;