6-124918651-C-T

Variant names:

• chr6-124918651-C-T
• rs812995
• ENST00000439075.1:n.740+1537G>A

Variant summary

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

The ENST00000439075.1(RNF217-AS1):​n.740+1537G>A variant causes a intron 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 ENST00000439075.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0330
• Publications: 1 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=-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 rank	MANE	Protein	UniProt
RNF217-AS1	NR_026876.1	n.728+1537G>A		intron_variant	Intron 6 of 6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
RNF217-AS1	ENST00000439075.1	n.740+1537G>A		intron_variant	Intron 6 of 6	1
RNF217-AS1	ENST00000655205.1	n.848+13045G>A		intron_variant	Intron 6 of 8
RNF217-AS1	ENST00000656500.1	n.843+13045G>A		intron_variant	Intron 6 of 7

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

African (AFR) AF: 0.649 AC: 26900 AN: 41420

American (AMR) AF: 0.836 AC: 12772 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.757 AC: 2626 AN: 3470

East Asian (EAS) AF: 0.999 AC: 5182 AN: 5186

South Asian (SAS) AF: 0.912 AC: 4393 AN: 4816

European-Finnish (FIN) AF: 0.845 AC: 8955 AN: 10598

Middle Eastern (MID) AF: 0.772 AC: 227 AN: 294

European-Non Finnish (NFE) AF: 0.811 AC: 55124 AN: 67982

Other (OTH) AF: 0.762 AC: 1610 AN: 2112

Alfa AF: 0.787 Hom.: 6140

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
PhyloP100		0.033

Splicing

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

Other links and lift over

dbSNP: rs812995; hg19: chr6-125239797;