chr3-113092581-G-A

Position:

• chr3-113092581-G-A

Variant summary

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

The ENST00000460707.1(NEPRO-AS1):​n.391-17521G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.745 in 152,018 control chromosomes in the GnomAD database, including 43,649 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 0.75 (43649 hom., cov: 31)
• Consequence: NEPRO-AS1 ENST00000460707.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.391

Genes affected

NEPRO-AS1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.841 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
NEPRO-AS1	NR_186655.1	n.414-17521G>A		intron_variant
NEPRO-AS1	NR_186656.1	n.414-15903G>A		intron_variant
NEPRO-AS1	NR_186657.1	n.190-15903G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
NEPRO-AS1	ENST00000460707.1	n.391-17521G>A		intron_variant		3
NEPRO-AS1	ENST00000496389.5	n.399+30571G>A		intron_variant		3
NEPRO-AS1	ENST00000655310.1	n.240-69353G>A		intron_variant

Frequencies

GnomAD3 genomes AF: 0.746 AC: 113267 AN: 151900 Hom.: 43634 Cov.: 31

Gnomad AFR AF: 0.578

Gnomad AMI AF: 0.885

Gnomad AMR AF: 0.796

Gnomad ASJ AF: 0.889

Gnomad EAS AF: 0.480

Gnomad SAS AF: 0.831

Gnomad FIN AF: 0.703

Gnomad MID AF: 0.845

Gnomad NFE AF: 0.847

Gnomad OTH AF: 0.771

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

GnomAD4 genome AF: 0.745 AC: 113327 AN: 152018 Hom.: 43649 Cov.: 31 AF XY: 0.739 AC XY: 54950 AN XY: 74316

Gnomad4 AFR AF: 0.578

Gnomad4 AMR AF: 0.796

Gnomad4 ASJ AF: 0.889

Gnomad4 EAS AF: 0.480

Gnomad4 SAS AF: 0.830

Gnomad4 FIN AF: 0.703

Gnomad4 NFE AF: 0.847

Gnomad4 OTH AF: 0.771

Alfa AF: 0.836 Hom.: 107046

Bravo AF: 0.742

Asia WGS AF: 0.681 AC: 2370 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	2.4
DANN	Benign	0.41

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7625411; hg19: chr3-112811428;