ENST00000815291.1:n.344-2883G>A

Variant names:

• chr3-132891908-G-A
• rs6439371
• ENST00000815291.1:n.344-2883G>A

Variant summary

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

The ENST00000815291.1(NPHP3-AS1):​n.344-2883G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.627 in 152,024 control chromosomes in the GnomAD database, including 29,866 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 0.63 (29866 hom., cov: 32)
• Consequence: NPHP3-AS1 ENST00000815291.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.14
• Publications: 26 publications found

Genes affected

NPHP3-AS1 (HGNC:24129): (NPHP3 antisense RNA 1)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.74).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.726 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000815291.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NPHP3-AS1	ENST00000815291.1		n.344-2883G>A		intron	N/A
	NPHP3-AS1	ENST00000815292.1		n.639-2883G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.627 AC: 95248 AN: 151906 Hom.: 29837 Cov.: 32

Gnomad AFR AF: 0.588

Gnomad AMI AF: 0.589

Gnomad AMR AF: 0.606

Gnomad ASJ AF: 0.646

Gnomad EAS AF: 0.747

Gnomad SAS AF: 0.588

Gnomad FIN AF: 0.639

Gnomad MID AF: 0.652

Gnomad NFE AF: 0.647

Gnomad OTH AF: 0.611

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

GnomAD4 genome AF: 0.627 AC: 95316 AN: 152024 Hom.: 29866 Cov.: 32 AF XY: 0.628 AC XY: 46655 AN XY: 74314

African (AFR) AF: 0.588 AC: 24365 AN: 41450

American (AMR) AF: 0.606 AC: 9247 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.646 AC: 2240 AN: 3468

East Asian (EAS) AF: 0.745 AC: 3858 AN: 5176

South Asian (SAS) AF: 0.588 AC: 2828 AN: 4810

European-Finnish (FIN) AF: 0.639 AC: 6747 AN: 10552

Middle Eastern (MID) AF: 0.656 AC: 193 AN: 294

European-Non Finnish (NFE) AF: 0.647 AC: 44009 AN: 67980

Other (OTH) AF: 0.612 AC: 1292 AN: 2112

Alfa AF: 0.639 Hom.: 132415

Bravo AF: 0.621

Asia WGS AF: 0.625 AC: 2174 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.74
CADD	Benign	9.0
DANN	Benign	0.53
PhyloP100		1.1

Splicing

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

Other links and lift over

dbSNP: rs6439371; hg19: chr3-132610752;