6-124887487-A-G

Variant names:

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

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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.

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
RNF217-AS1	ENST00000655205.1	n.848+44209T>C		intron_variant	Intron 6 of 8
RNF217-AS1	ENST00000656500.1	n.843+44209T>C		intron_variant	Intron 6 of 7
RNF217-AS1	ENST00000657116.1	n.190+44209T>C		intron_variant	Intron 3 of 3

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

Gnomad4 AFR AF: 0.702

Gnomad4 AMR AF: 0.897

Gnomad4 ASJ AF: 0.853

Gnomad4 EAS AF: 1.00

Gnomad4 SAS AF: 0.953

Gnomad4 FIN AF: 0.908

Gnomad4 NFE AF: 0.894

Gnomad4 OTH AF: 0.844

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 v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.8
DANN	Benign	0.59

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs781718; hg19: chr6-125208633;