6-124835303-C-T

Variant names:

• chr6-124835303-C-T
• rs11154271
• ENST00000655205.1:n.849-48773G>A

Variant summary

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

The ENST00000655205.1(RNF217-AS1):​n.849-48773G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.825 in 151,932 control chromosomes in the GnomAD database, including 52,030 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 0.83 (52030 hom., cov: 30)
• Consequence: RNF217-AS1 ENST00000655205.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.685
• Publications: 6 publications found

Genes affected

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

ENSG00000304495 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.925 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.849-48773G>A		intron_variant	Intron 6 of 8
RNF217-AS1	ENST00000656500.1	n.844-8756G>A		intron_variant	Intron 6 of 7
RNF217-AS1	ENST00000657116.1	n.191-8756G>A		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.825 AC: 125298 AN: 151814 Hom.: 51968 Cov.: 30

Gnomad AFR AF: 0.898

Gnomad AMI AF: 0.754

Gnomad AMR AF: 0.793

Gnomad ASJ AF: 0.751

Gnomad EAS AF: 0.947

Gnomad SAS AF: 0.732

Gnomad FIN AF: 0.805

Gnomad MID AF: 0.759

Gnomad NFE AF: 0.794

Gnomad OTH AF: 0.812

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

GnomAD4 genome AF: 0.825 AC: 125415 AN: 151932 Hom.: 52030 Cov.: 30 AF XY: 0.824 AC XY: 61224 AN XY: 74256

African (AFR) AF: 0.898 AC: 37238 AN: 41472

American (AMR) AF: 0.793 AC: 12094 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.751 AC: 2606 AN: 3468

East Asian (EAS) AF: 0.947 AC: 4890 AN: 5164

South Asian (SAS) AF: 0.732 AC: 3519 AN: 4810

European-Finnish (FIN) AF: 0.805 AC: 8463 AN: 10514

Middle Eastern (MID) AF: 0.765 AC: 225 AN: 294

European-Non Finnish (NFE) AF: 0.794 AC: 53976 AN: 67942

Other (OTH) AF: 0.814 AC: 1718 AN: 2110

Alfa AF: 0.803 Hom.: 187314

Bravo AF: 0.829

Asia WGS AF: 0.836 AC: 2890 AN: 3462

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	1.7
DANN	Benign	0.26
PhyloP100		0.69

Splicing

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

Other links and lift over

dbSNP: rs11154271; hg19: chr6-125156449;