3-113141933-A-G

Variant names:

• chr3-113141933-A-G
• rs2613964
• ENST00000496389.5:n.400-20001A>G

Variant summary

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

The ENST00000496389.5(NEPRO-AS1):​n.400-20001A>G variant causes a intron 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 ENST00000496389.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.329
• Publications: 6 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
NEPRO-AS1	NR_186659.1	n.190-1921A>G		intron_variant	Intron 1 of 1
NEPRO-AS1	NR_186660.1	n.414-1921A>G		intron_variant	Intron 2 of 2
NEPRO-AS1	NR_186661.1	n.414-20001A>G		intron_variant	Intron 2 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
NEPRO-AS1	ENST00000496389.5	n.400-20001A>G		intron_variant	Intron 2 of 3	3
NEPRO-AS1	ENST00000655310.1	n.240-20001A>G		intron_variant	Intron 1 of 2
NEPRO-AS1	ENST00000686071.1	n.447-20001A>G		intron_variant	Intron 2 of 3

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

African (AFR) AF: 0.594 AC: 24625 AN: 41476

American (AMR) AF: 0.508 AC: 7757 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.661 AC: 2293 AN: 3468

East Asian (EAS) AF: 0.640 AC: 3298 AN: 5156

South Asian (SAS) AF: 0.639 AC: 3083 AN: 4826

European-Finnish (FIN) AF: 0.665 AC: 7036 AN: 10574

Middle Eastern (MID) AF: 0.622 AC: 183 AN: 294

European-Non Finnish (NFE) AF: 0.652 AC: 44341 AN: 67962

Other (OTH) AF: 0.604 AC: 1278 AN: 2116

Alfa AF: 0.631 Hom.: 40178

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
PhyloP100		-0.33

Splicing

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

Other links and lift over

dbSNP: rs2613964; hg19: chr3-112860780;