chr3-113092361-A-G

Position:

• chr3-113092361-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.240-69573A>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 0.323 in 152,040 control chromosomes in the GnomAD database, including 9,739 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 0.32 (9739 hom., cov: 31)
• Consequence: NEPRO-AS1 ENST00000655310.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0610

Genes affected

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

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.45 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
NEPRO-AS1	ENST00000655310.1	n.240-69573A>G		intron_variant, non_coding_transcript_variant
	ENST00000691778.1	n.106+11956T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.324 AC: 49169 AN: 151922 Hom.: 9745 Cov.: 31

Gnomad AFR AF: 0.0936

Gnomad AMI AF: 0.394

Gnomad AMR AF: 0.341

Gnomad ASJ AF: 0.446

Gnomad EAS AF: 0.191

Gnomad SAS AF: 0.391

Gnomad FIN AF: 0.336

Gnomad MID AF: 0.481

Gnomad NFE AF: 0.454

Gnomad OTH AF: 0.369

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

GnomAD4 genome AF: 0.323 AC: 49162 AN: 152040 Hom.: 9739 Cov.: 31 AF XY: 0.321 AC XY: 23878 AN XY: 74326

Gnomad4 AFR AF: 0.0934

Gnomad4 AMR AF: 0.341

Gnomad4 ASJ AF: 0.446

Gnomad4 EAS AF: 0.191

Gnomad4 SAS AF: 0.391

Gnomad4 FIN AF: 0.336

Gnomad4 NFE AF: 0.454

Gnomad4 OTH AF: 0.366

Alfa AF: 0.433 Hom.: 30093

Bravo AF: 0.311

Asia WGS AF: 0.243 AC: 847 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.93
DANN	Benign	0.68

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7647147; hg19: chr3-112811208;