chr6-124918651-C-T

Position:

• chr6-124918651-C-T

Variant summary

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

The NR_026876.1(RNF217-AS1):​n.728+1537G>A 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 0.779 in 152,068 control chromosomes in the GnomAD database, including 46,915 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 0.78 (46915 hom., cov: 32)
• Consequence: RNF217-AS1 NR_026876.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0330

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=-0.82).
• 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
RNF217-AS1	NR_026876.1	n.728+1537G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
RNF217-AS1	ENST00000663792.1	n.535+13045G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.779 AC: 118351 AN: 151950 Hom.: 46867 Cov.: 32

Gnomad AFR AF: 0.649

Gnomad AMI AF: 0.737

Gnomad AMR AF: 0.836

Gnomad ASJ AF: 0.757

Gnomad EAS AF: 0.999

Gnomad SAS AF: 0.913

Gnomad FIN AF: 0.845

Gnomad MID AF: 0.756

Gnomad NFE AF: 0.811

Gnomad OTH AF: 0.760

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

GnomAD4 genome AF: 0.779 AC: 118460 AN: 152068 Hom.: 46915 Cov.: 32 AF XY: 0.785 AC XY: 58400 AN XY: 74364

Gnomad4 AFR AF: 0.649

Gnomad4 AMR AF: 0.836

Gnomad4 ASJ AF: 0.757

Gnomad4 EAS AF: 0.999

Gnomad4 SAS AF: 0.912

Gnomad4 FIN AF: 0.845

Gnomad4 NFE AF: 0.811

Gnomad4 OTH AF: 0.762

Alfa AF: 0.792 Hom.: 5970

Bravo AF: 0.770

Asia WGS AF: 0.924 AC: 3208 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	4.3
DANN	Benign	0.42

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs812995; hg19: chr6-125239797;