ENST00000496389.5:n.400-41836A>G

Variant names:

• chr3-113120098-A-G
• rs1461106
• ENST00000496389.5:n.400-41836A>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.400-41836A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.16 in 152,152 control chromosomes in the GnomAD database, including 2,177 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 0.16 (2177 hom., cov: 32)
• Consequence: NEPRO-AS1 ENST00000496389.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.779
• Publications: 3 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=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.232 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
NEPRO-AS1	NR_186659.1	n.190-23756A>G		intron_variant	Intron 1 of 1
NEPRO-AS1	NR_186660.1	n.414-23756A>G		intron_variant	Intron 2 of 2
NEPRO-AS1	NR_186661.1	n.414-41836A>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.400-41836A>G		intron_variant	Intron 2 of 3	3
NEPRO-AS1	ENST00000655310.1	n.240-41836A>G		intron_variant	Intron 1 of 2
NEPRO-AS1	ENST00000686071.1	n.447-41836A>G		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.160 AC: 24373 AN: 152034 Hom.: 2174 Cov.: 32

Gnomad AFR AF: 0.236

Gnomad AMI AF: 0.106

Gnomad AMR AF: 0.114

Gnomad ASJ AF: 0.135

Gnomad EAS AF: 0.0327

Gnomad SAS AF: 0.121

Gnomad FIN AF: 0.113

Gnomad MID AF: 0.171

Gnomad NFE AF: 0.147

Gnomad OTH AF: 0.146

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

GnomAD4 genome AF: 0.160 AC: 24390 AN: 152152 Hom.: 2177 Cov.: 32 AF XY: 0.156 AC XY: 11619 AN XY: 74392

African (AFR) AF: 0.236 AC: 9771 AN: 41474

American (AMR) AF: 0.114 AC: 1746 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.135 AC: 467 AN: 3472

East Asian (EAS) AF: 0.0324 AC: 168 AN: 5180

South Asian (SAS) AF: 0.121 AC: 586 AN: 4834

European-Finnish (FIN) AF: 0.113 AC: 1200 AN: 10594

Middle Eastern (MID) AF: 0.173 AC: 51 AN: 294

European-Non Finnish (NFE) AF: 0.147 AC: 10000 AN: 68000

Other (OTH) AF: 0.144 AC: 304 AN: 2112

Alfa AF: 0.146 Hom.: 3040

Bravo AF: 0.162

Asia WGS AF: 0.0810 AC: 283 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.75
DANN	Benign	0.27
PhyloP100		-0.78

Splicing

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

Other links and lift over

dbSNP: rs1461106; hg19: chr3-112838945;