3-113162692-G-T

Variant names:

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

Variant summary

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

The ENST00000490139.1(LINC02044):​n.299+2435C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.201 in 152,084 control chromosomes in the GnomAD database, including 4,441 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 0.20 (4441 hom., cov: 32)
• Consequence: LINC02044 ENST00000490139.1 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: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.425 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000490139.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02044	NR_110823.1		n.211+2435C>A		intron	N/A
	NEPRO-AS1	NR_186661.1		n.499+673G>T		intron	N/A
	NEPRO-AS1	NR_186662.1		n.190-20361G>T		intron	N/A

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.201 AC: 30569 AN: 151964 Hom.: 4433 Cov.: 32

Gnomad AFR AF: 0.382

Gnomad AMI AF: 0.0746

Gnomad AMR AF: 0.160

Gnomad ASJ AF: 0.0771

Gnomad EAS AF: 0.440

Gnomad SAS AF: 0.162

Gnomad FIN AF: 0.197

Gnomad MID AF: 0.0823

Gnomad NFE AF: 0.0950

Gnomad OTH AF: 0.173

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

GnomAD4 genome AF: 0.201 AC: 30607 AN: 152084 Hom.: 4441 Cov.: 32 AF XY: 0.204 AC XY: 15167 AN XY: 74338

African (AFR) AF: 0.382 AC: 15823 AN: 41444

American (AMR) AF: 0.160 AC: 2451 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.0771 AC: 267 AN: 3464

East Asian (EAS) AF: 0.441 AC: 2281 AN: 5178

South Asian (SAS) AF: 0.162 AC: 782 AN: 4820

European-Finnish (FIN) AF: 0.197 AC: 2084 AN: 10556

Middle Eastern (MID) AF: 0.0816 AC: 24 AN: 294

European-Non Finnish (NFE) AF: 0.0950 AC: 6463 AN: 68010

Other (OTH) AF: 0.172 AC: 364 AN: 2112

Alfa AF: 0.125 Hom.: 7233

Bravo AF: 0.208

Asia WGS AF: 0.273 AC: 949 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.1
DANN	Benign	0.30
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;