rs1461106

chr3-113120098-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.240-41836A>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 0.16 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 ENST00000655310.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.779

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=-0.96).
• 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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
NEPRO-AS1	ENST00000655310.1	n.240-41836A>G		intron_variant, non_coding_transcript_variant
NEPRO-AS1	ENST00000496389.5	n.400-41836A>G		intron_variant, non_coding_transcript_variant		3
NEPRO-AS1	ENST00000686071.1	n.447-41836A>G		intron_variant, non_coding_transcript_variant
NEPRO-AS1	ENST00000700984.1	n.236-41836A>G		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.236

Gnomad4 AMR AF: 0.114

Gnomad4 ASJ AF: 0.135

Gnomad4 EAS AF: 0.0324

Gnomad4 SAS AF: 0.121

Gnomad4 FIN AF: 0.113

Gnomad4 NFE AF: 0.147

Gnomad4 OTH AF: 0.144

Alfa AF: 0.143 Hom.: 2293

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1461106; hg19: chr3-112838945;