rs299247

Variant names:

• chr18-22709809-C-T
• rs299247
• ENST00000578831.1:n.288-4889G>A

Variant summary

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

The ENST00000578831.1(RBBP8-AS1):​n.288-4889G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.239 in 152,108 control chromosomes in the GnomAD database, including 6,417 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 0.24 (6417 hom., cov: 32)
• Consequence: RBBP8-AS1 ENST00000578831.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.196
• Publications: 6 publications found

Genes affected

RBBP8-AS1 (HGNC:58091):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.477 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000578831.1. 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
	RBBP8-AS1	ENST00000578831.1	TSL:4	n.288-4889G>A		intron	N/A
	RBBP8-AS1	ENST00000716263.1		n.536-4889G>A		intron	N/A
	RBBP8-AS1	ENST00000716264.1		n.436-4889G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.239 AC: 36302 AN: 151988 Hom.: 6387 Cov.: 32

Gnomad AFR AF: 0.482

Gnomad AMI AF: 0.102

Gnomad AMR AF: 0.207

Gnomad ASJ AF: 0.107

Gnomad EAS AF: 0.372

Gnomad SAS AF: 0.287

Gnomad FIN AF: 0.0750

Gnomad MID AF: 0.218

Gnomad NFE AF: 0.120

Gnomad OTH AF: 0.202

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

GnomAD4 genome AF: 0.239 AC: 36385 AN: 152108 Hom.: 6417 Cov.: 32 AF XY: 0.238 AC XY: 17729 AN XY: 74366

African (AFR) AF: 0.483 AC: 20007 AN: 41442

American (AMR) AF: 0.207 AC: 3156 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.107 AC: 370 AN: 3468

East Asian (EAS) AF: 0.372 AC: 1919 AN: 5160

South Asian (SAS) AF: 0.286 AC: 1379 AN: 4818

European-Finnish (FIN) AF: 0.0750 AC: 796 AN: 10610

Middle Eastern (MID) AF: 0.211 AC: 62 AN: 294

European-Non Finnish (NFE) AF: 0.120 AC: 8168 AN: 68012

Other (OTH) AF: 0.206 AC: 435 AN: 2112

Alfa AF: 0.153 Hom.: 4017

Bravo AF: 0.258

Asia WGS AF: 0.363 AC: 1265 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	15
DANN	Benign	0.62
PhyloP100		0.20

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: rs299247;

hg19: chr18-20289772;