3-132769910-T-C

Position:

• chr3-132769910-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000504440.1(NPHP3-AS1):​n.250-23624T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.337 in 151,916 control chromosomes in the GnomAD database, including 8,865 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 0.34 (8865 hom., cov: 32)
• Consequence: NPHP3-AS1 ENST00000504440.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.152

Genes affected

NPHP3-AS1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• 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/exons	MANE	Protein	UniProt
NPHP3-AS1	NR_002811.2	n.842-23624T>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
NPHP3-AS1	ENST00000504440.1	n.250-23624T>C		intron_variant		1

Frequencies

GnomAD3 genomes AF: 0.337 AC: 51120 AN: 151798 Hom.: 8862 Cov.: 32

Gnomad AFR AF: 0.329

Gnomad AMI AF: 0.395

Gnomad AMR AF: 0.294

Gnomad ASJ AF: 0.369

Gnomad EAS AF: 0.563

Gnomad SAS AF: 0.407

Gnomad FIN AF: 0.330

Gnomad MID AF: 0.449

Gnomad NFE AF: 0.327

Gnomad OTH AF: 0.350

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

GnomAD4 genome AF: 0.337 AC: 51160 AN: 151916 Hom.: 8865 Cov.: 32 AF XY: 0.338 AC XY: 25092 AN XY: 74232

Gnomad4 AFR AF: 0.329

Gnomad4 AMR AF: 0.294

Gnomad4 ASJ AF: 0.369

Gnomad4 EAS AF: 0.563

Gnomad4 SAS AF: 0.407

Gnomad4 FIN AF: 0.330

Gnomad4 NFE AF: 0.327

Gnomad4 OTH AF: 0.348

Alfa AF: 0.329 Hom.: 8232

Bravo AF: 0.335

Asia WGS AF: 0.471 AC: 1634 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	3.4
DANN	Benign	0.88

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9879204; hg19: chr3-132488754;