XR_242624.4:n.685+1551G>A

Variant names:

• chr9-74171381-C-T
• rs10746936
• ENST00000715876.1:n.685+1551G>A

Variant summary

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

The XR_242624.4(LOC101927329):​n.685+1551G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.488 in 151,984 control chromosomes in the GnomAD database, including 18,254 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 0.49 (18254 hom., cov: 31)
• Consequence: LOC101927329 XR_242624.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.04
• Publications: 1 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=-1.02).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.553 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.685+1551G>A		intron	N/A
	RORB-AS1	ENST00000722221.1		n.686+1551G>A		intron	N/A
	RORB-AS1	ENST00000722222.1		n.782+1551G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.488 AC: 74091 AN: 151864 Hom.: 18237 Cov.: 31

Gnomad AFR AF: 0.457

Gnomad AMI AF: 0.595

Gnomad AMR AF: 0.562

Gnomad ASJ AF: 0.550

Gnomad EAS AF: 0.556

Gnomad SAS AF: 0.546

Gnomad FIN AF: 0.409

Gnomad MID AF: 0.582

Gnomad NFE AF: 0.487

Gnomad OTH AF: 0.518

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

GnomAD4 genome AF: 0.488 AC: 74159 AN: 151984 Hom.: 18254 Cov.: 31 AF XY: 0.488 AC XY: 36292 AN XY: 74296

African (AFR) AF: 0.457 AC: 18919 AN: 41418

American (AMR) AF: 0.562 AC: 8588 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.550 AC: 1905 AN: 3462

East Asian (EAS) AF: 0.556 AC: 2873 AN: 5166

South Asian (SAS) AF: 0.547 AC: 2637 AN: 4820

European-Finnish (FIN) AF: 0.409 AC: 4321 AN: 10560

Middle Eastern (MID) AF: 0.575 AC: 169 AN: 294

European-Non Finnish (NFE) AF: 0.487 AC: 33116 AN: 67970

Other (OTH) AF: 0.515 AC: 1090 AN: 2116

Alfa AF: 0.491 Hom.: 58457

Bravo AF: 0.498

Asia WGS AF: 0.488 AC: 1697 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.083
DANN	Benign	0.25
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs10746936; hg19: chr9-76786297; COSMIC: COSV60360690;