chr3-113162692-G-A

Variant names:

• chr3-113162692-G-A
• rs9881633
• ENST00000463017.1:n.182+673G>A

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The ENST00000463017.1(NEPRO-AS1):​n.182+673G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 32)
• Consequence: NEPRO-AS1 ENST00000463017.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0420
• Publications: 2 publications found

Genes affected

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

LINC02044 (HGNC:52884): (long intergenic non-protein coding RNA 2044)

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000463017.1. 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
	LINC02044	NR_110823.1		n.211+2435C>T		intron	N/A
	NEPRO-AS1	NR_186661.1		n.499+673G>A		intron	N/A
	NEPRO-AS1	NR_186662.1		n.190-20361G>A		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NEPRO-AS1	ENST00000463017.1	TSL:3	n.182+673G>A		intron	N/A
	LINC02044	ENST00000490139.1	TSL:2	n.299+2435C>T		intron	N/A
	NEPRO-AS1	ENST00000496389.5	TSL:3	n.485+673G>A		intron	N/A

Frequencies

GnomAD3 genomes Cov.: 32

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

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.3
DANN	Benign	0.29
PhyloP100		-0.042

Splicing

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

Other links and lift over

dbSNP: rs9881633; hg19: chr3-112881539;