3-132769910-T-C

Variant names:

• chr3-132769910-T-C
• rs9879204
• ENST00000504440.1:n.250-23624T>C

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 5 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=-0.94).
• 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 rank	MANE	Protein	UniProt
NPHP3-AS1	NR_002811.2	n.842-23624T>C		intron_variant	Intron 3 of 10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
NPHP3-AS1	ENST00000504440.1	n.250-23624T>C		intron_variant	Intron 3 of 10	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

African (AFR) AF: 0.329 AC: 13629 AN: 41404

American (AMR) AF: 0.294 AC: 4485 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.369 AC: 1277 AN: 3464

East Asian (EAS) AF: 0.563 AC: 2913 AN: 5172

South Asian (SAS) AF: 0.407 AC: 1959 AN: 4816

European-Finnish (FIN) AF: 0.330 AC: 3472 AN: 10536

Middle Eastern (MID) AF: 0.459 AC: 135 AN: 294

European-Non Finnish (NFE) AF: 0.327 AC: 22201 AN: 67962

Other (OTH) AF: 0.348 AC: 730 AN: 2100

Alfa AF: 0.329 Hom.: 10670

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
PhyloP100		-0.15

Splicing

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

Other links and lift over

dbSNP: rs9879204; hg19: chr3-132488754;