6-124887487-A-G

Position:

• chr6-124887487-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000663792.1(RNF217-AS1):​n.535+44209T>C variant causes a intron, non coding transcript 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 ENST00000663792.1 intron, non_coding_transcript
• 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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
RNF217-AS1	ENST00000663792.1	n.535+44209T>C		intron_variant, non_coding_transcript_variant

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;