6-124887487-A-G

Variant names:

• chr6-124887487-A-G
• rs781718
• ENST00000655205.1:n.848+44209T>C

Variant summary

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

The ENST00000655205.1(RNF217-AS1):​n.848+44209T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.847 in 151,790 control chromosomes in the GnomAD database, including 55,101 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 0.85 (55101 hom., cov: 28)
• Consequence: RNF217-AS1 ENST00000655205.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.574
• Publications: 2 publications found

Genes affected

RNF217-AS1 (HGNC:50866): (RNF217 antisense RNA 1 (head to head))

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.977 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000655205.1. 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
	RNF217-AS1	ENST00000655205.1		n.848+44209T>C		intron	N/A
	RNF217-AS1	ENST00000656500.1		n.843+44209T>C		intron	N/A
	RNF217-AS1	ENST00000657116.1		n.190+44209T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.847 AC: 128479 AN: 151674 Hom.: 55068 Cov.: 28

Gnomad AFR AF: 0.702

Gnomad AMI AF: 0.980

Gnomad AMR AF: 0.896

Gnomad ASJ AF: 0.853

Gnomad EAS AF: 1.00

Gnomad SAS AF: 0.952

Gnomad FIN AF: 0.908

Gnomad MID AF: 0.810

Gnomad NFE AF: 0.894

Gnomad OTH AF: 0.842

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

GnomAD4 genome AF: 0.847 AC: 128572 AN: 151790 Hom.: 55101 Cov.: 28 AF XY: 0.852 AC XY: 63201 AN XY: 74164

African (AFR) AF: 0.702 AC: 28983 AN: 41296

American (AMR) AF: 0.897 AC: 13688 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.853 AC: 2957 AN: 3468

East Asian (EAS) AF: 1.00 AC: 5108 AN: 5110

South Asian (SAS) AF: 0.953 AC: 4580 AN: 4808

European-Finnish (FIN) AF: 0.908 AC: 9610 AN: 10586

Middle Eastern (MID) AF: 0.816 AC: 240 AN: 294

European-Non Finnish (NFE) AF: 0.894 AC: 60735 AN: 67944

Other (OTH) AF: 0.844 AC: 1779 AN: 2108

Alfa AF: 0.851 Hom.: 3980

Bravo AF: 0.838

Asia WGS AF: 0.952 AC: 3311 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	1.8
DANN	Benign	0.59
PhyloP100		-0.57

Splicing

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

Other links and lift over

dbSNP: rs781718; hg19: chr6-125208633;