rs4017724

Variant names:

• chr3-132759389-G-A
• rs4017724
• ENST00000504440.1:n.249+25945G>A

Variant summary

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

The ENST00000504440.1(NPHP3-AS1):​n.249+25945G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.302 in 151,898 control chromosomes in the GnomAD database, including 7,445 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 0.30 (7445 hom., cov: 32)
• Consequence: NPHP3-AS1 ENST00000504440.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.291
• Publications: 4 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=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.546 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
NPHP3-AS1	NR_002811.2	n.841+25945G>A		intron_variant	Intron 3 of 10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
NPHP3-AS1	ENST00000504440.1	n.249+25945G>A		intron_variant	Intron 3 of 10	1

Frequencies

GnomAD3 genomes AF: 0.302 AC: 45911 AN: 151780 Hom.: 7451 Cov.: 32

Gnomad AFR AF: 0.211

Gnomad AMI AF: 0.395

Gnomad AMR AF: 0.279

Gnomad ASJ AF: 0.363

Gnomad EAS AF: 0.563

Gnomad SAS AF: 0.406

Gnomad FIN AF: 0.331

Gnomad MID AF: 0.427

Gnomad NFE AF: 0.326

Gnomad OTH AF: 0.317

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

GnomAD4 genome AF: 0.302 AC: 45909 AN: 151898 Hom.: 7445 Cov.: 32 AF XY: 0.305 AC XY: 22615 AN XY: 74208

African (AFR) AF: 0.211 AC: 8754 AN: 41438

American (AMR) AF: 0.279 AC: 4260 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.363 AC: 1257 AN: 3466

East Asian (EAS) AF: 0.563 AC: 2913 AN: 5176

South Asian (SAS) AF: 0.406 AC: 1950 AN: 4808

European-Finnish (FIN) AF: 0.331 AC: 3477 AN: 10510

Middle Eastern (MID) AF: 0.432 AC: 127 AN: 294

European-Non Finnish (NFE) AF: 0.326 AC: 22150 AN: 67924

Other (OTH) AF: 0.313 AC: 662 AN: 2112

Alfa AF: 0.302 Hom.: 1165

Bravo AF: 0.295

Asia WGS AF: 0.453 AC: 1568 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.84
DANN	Benign	0.33
PhyloP100		-0.29

Splicing

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

Other links and lift over

dbSNP: rs4017724; hg19: chr3-132478233;