3-113141933-A-G

Variant summary

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

The ENST00000655310.1(NEPRO-AS1):n.240-20001A>G 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 0.62 in 152,058 control chromosomes in the GnomAD database, including 29,543 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 0.62 (29543 hom., cov: 32)
• Consequence: NEPRO-AS1 ENST00000655310.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.329

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.647 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
NEPRO-AS1	ENST00000655310.1	n.240-20001A>G		intron_variant, non_coding_transcript_variant
NEPRO-AS1	ENST00000496389.5	n.400-20001A>G		intron_variant, non_coding_transcript_variant		3
NEPRO-AS1	ENST00000686071.1	n.447-20001A>G		intron_variant, non_coding_transcript_variant
NEPRO-AS1	ENST00000700984.1	n.236-20001A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.620 AC: 94251 AN: 151940 Hom.: 29535 Cov.: 32

Gnomad AFR AF: 0.594

Gnomad AMI AF: 0.437

Gnomad AMR AF: 0.508

Gnomad ASJ AF: 0.661

Gnomad EAS AF: 0.640

Gnomad SAS AF: 0.637

Gnomad FIN AF: 0.665

Gnomad MID AF: 0.627

Gnomad NFE AF: 0.652

Gnomad OTH AF: 0.611

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

GnomAD4 genome AF: 0.620 AC: 94292 AN: 152058 Hom.: 29543 Cov.: 32 AF XY: 0.620 AC XY: 46038 AN XY: 74310

Gnomad4 AFR AF: 0.594

Gnomad4 AMR AF: 0.508

Gnomad4 ASJ AF: 0.661

Gnomad4 EAS AF: 0.640

Gnomad4 SAS AF: 0.639

Gnomad4 FIN AF: 0.665

Gnomad4 NFE AF: 0.652

Gnomad4 OTH AF: 0.604

Alfa AF: 0.635 Hom.: 31212

Bravo AF: 0.605

Asia WGS AF: 0.583 AC: 2020 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
Cadd	Benign	2.0
Dann	Benign	0.72

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2613964; hg19: chr3-112860780;