rs7647147

Variant names:

• chr3-113092361-A-G
• rs7647147
• ENST00000460707.1:n.391-17741A>G

Variant summary

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

The ENST00000460707.1(NEPRO-AS1):​n.391-17741A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.323 in 152,040 control chromosomes in the GnomAD database, including 9,739 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 0.32 (9739 hom., cov: 31)
• Consequence: NEPRO-AS1 ENST00000460707.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0610
• Publications: 7 publications found

Genes affected

NEPRO-AS1 (HGNC:41049): (NEPRO antisense RNA 1)

LOLI1 (HGNC:56775):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.45 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000460707.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NEPRO-AS1	NR_186655.1		n.414-17741A>G		intron	N/A
	NEPRO-AS1	NR_186656.1		n.414-16123A>G		intron	N/A
	NEPRO-AS1	NR_186657.1		n.190-16123A>G		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NEPRO-AS1	ENST00000460707.1	TSL:3	n.391-17741A>G		intron	N/A
	NEPRO-AS1	ENST00000496389.5	TSL:3	n.399+30351A>G		intron	N/A
	NEPRO-AS1	ENST00000655310.1		n.240-69573A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.324 AC: 49169 AN: 151922 Hom.: 9745 Cov.: 31

Gnomad AFR AF: 0.0936

Gnomad AMI AF: 0.394

Gnomad AMR AF: 0.341

Gnomad ASJ AF: 0.446

Gnomad EAS AF: 0.191

Gnomad SAS AF: 0.391

Gnomad FIN AF: 0.336

Gnomad MID AF: 0.481

Gnomad NFE AF: 0.454

Gnomad OTH AF: 0.369

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

GnomAD4 genome AF: 0.323 AC: 49162 AN: 152040 Hom.: 9739 Cov.: 31 AF XY: 0.321 AC XY: 23878 AN XY: 74326

African (AFR) AF: 0.0934 AC: 3874 AN: 41488

American (AMR) AF: 0.341 AC: 5206 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.446 AC: 1547 AN: 3472

East Asian (EAS) AF: 0.191 AC: 990 AN: 5170

South Asian (SAS) AF: 0.391 AC: 1887 AN: 4822

European-Finnish (FIN) AF: 0.336 AC: 3546 AN: 10550

Middle Eastern (MID) AF: 0.469 AC: 137 AN: 292

European-Non Finnish (NFE) AF: 0.454 AC: 30848 AN: 67954

Other (OTH) AF: 0.366 AC: 770 AN: 2102

Alfa AF: 0.410 Hom.: 43717

Bravo AF: 0.311

Asia WGS AF: 0.243 AC: 847 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.93
DANN	Benign	0.68
PhyloP100		-0.061

Splicing

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

Other links and lift over

dbSNP: rs7647147; hg19: chr3-112811208;