rs1452142

Variant names:

• chr3-132894632-A-T
• rs1452142
• ENST00000815291.1:n.344-159A>T

Variant summary

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

The ENST00000815291.1(NPHP3-AS1):​n.344-159A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.386 in 151,810 control chromosomes in the GnomAD database, including 12,118 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 0.39 (12118 hom., cov: 31)
• Consequence: NPHP3-AS1 ENST00000815291.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.62
• Publications: 0 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=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.458 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
NPHP3-AS1	ENST00000815291.1	n.344-159A>T		intron_variant	Intron 3 of 3
NPHP3-AS1	ENST00000815292.1	n.639-159A>T		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.386 AC: 58583 AN: 151700 Hom.: 12113 Cov.: 31

Gnomad AFR AF: 0.271

Gnomad AMI AF: 0.374

Gnomad AMR AF: 0.443

Gnomad ASJ AF: 0.390

Gnomad EAS AF: 0.0603

Gnomad SAS AF: 0.379

Gnomad FIN AF: 0.431

Gnomad MID AF: 0.399

Gnomad NFE AF: 0.462

Gnomad OTH AF: 0.383

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

GnomAD4 genome AF: 0.386 AC: 58596 AN: 151810 Hom.: 12118 Cov.: 31 AF XY: 0.386 AC XY: 28647 AN XY: 74184

African (AFR) AF: 0.271 AC: 11205 AN: 41402

American (AMR) AF: 0.443 AC: 6752 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.390 AC: 1353 AN: 3468

East Asian (EAS) AF: 0.0604 AC: 313 AN: 5182

South Asian (SAS) AF: 0.380 AC: 1823 AN: 4798

European-Finnish (FIN) AF: 0.431 AC: 4519 AN: 10480

Middle Eastern (MID) AF: 0.408 AC: 119 AN: 292

European-Non Finnish (NFE) AF: 0.462 AC: 31363 AN: 67914

Other (OTH) AF: 0.383 AC: 809 AN: 2112

Alfa AF: 0.421 Hom.: 1709

Bravo AF: 0.379

Asia WGS AF: 0.222 AC: 774 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.84
DANN	Benign	0.78
PhyloP100		-1.6

Splicing

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

Other links and lift over

dbSNP: rs1452142; hg19: chr3-132613476; COSMIC: COSV60112508;