chr3-132681258-C-CT

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBA1

The NM_153240.5(NPHP3):​c.*651_*652insA variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0238 in 105,608 control chromosomes in the GnomAD database, including 49 homozygotes. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.024 ( 49 hom., cov: 23)
Exomes 𝑓: 0.027 ( 0 hom. )

Consequence

NPHP3
NM_153240.5 3_prime_UTR

Scores

Not classified

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 1.19
Variant links:
Genes affected
NPHP3 (HGNC:7907): (nephrocystin 3) This gene encodes a protein containing a coiled-coil (CC) domain, a tubulin-tyrosine ligase (TTL) domain, and a tetratrico peptide repeat (TPR) domain. The encoded protein interacts with nephrocystin, it is required for normal ciliary development, and it functions in renal tubular development. Mutations in this gene are associated with nephronophthisis type 3, and also with renal-hepatic-pancreatic dysplasia, and Meckel syndrome type 7. Naturally occurring read-through transcripts exist between this gene and the downstream ACAD11 (acyl-CoA dehydrogenase family, member 11) gene. [provided by RefSeq, Feb 2011]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP6
Variant 3-132681258-C-CT is Benign according to our data. Variant chr3-132681258-C-CT is described in ClinVar as [Benign]. Clinvar id is 1264737.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0517 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
NPHP3NM_153240.5 linkuse as main transcriptc.*651_*652insA 3_prime_UTR_variant 27/27 ENST00000337331.10 NP_694972.3
NPHP3-ACAD11NR_037804.1 linkuse as main transcriptn.3995+655_3995+656insA intron_variant, non_coding_transcript_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
NPHP3ENST00000337331.10 linkuse as main transcriptc.*651_*652insA 3_prime_UTR_variant 27/271 NM_153240.5 ENSP00000338766 P1Q7Z494-1
NPHP3ENST00000474871.5 linkuse as main transcriptn.3843_3844insA non_coding_transcript_exon_variant 11/112
NPHP3ENST00000493732.5 linkuse as main transcript downstream_gene_variant 2

Frequencies

GnomAD3 genomes
AF:
0.0238
AC:
2512
AN:
105526
Hom.:
48
Cov.:
23
show subpopulations
Gnomad AFR
AF:
0.0540
Gnomad AMI
AF:
0.0164
Gnomad AMR
AF:
0.0116
Gnomad ASJ
AF:
0.00969
Gnomad EAS
AF:
0.00369
Gnomad SAS
AF:
0.00603
Gnomad FIN
AF:
0.000715
Gnomad MID
AF:
0.0155
Gnomad NFE
AF:
0.0152
Gnomad OTH
AF:
0.0204
GnomAD4 exome
AF:
0.0270
AC:
2
AN:
74
Hom.:
0
Cov.:
0
AF XY:
0.0370
AC XY:
2
AN XY:
54
show subpopulations
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.0152
Gnomad4 OTH exome
AF:
0.500
GnomAD4 genome
AF:
0.0238
AC:
2512
AN:
105534
Hom.:
49
Cov.:
23
AF XY:
0.0219
AC XY:
1076
AN XY:
49058
show subpopulations
Gnomad4 AFR
AF:
0.0540
Gnomad4 AMR
AF:
0.0116
Gnomad4 ASJ
AF:
0.00969
Gnomad4 EAS
AF:
0.00370
Gnomad4 SAS
AF:
0.00606
Gnomad4 FIN
AF:
0.000715
Gnomad4 NFE
AF:
0.0152
Gnomad4 OTH
AF:
0.0203

ClinVar

Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not provided Benign:1
Benign, criteria provided, single submitterclinical testingGeneDxJun 04, 2021- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction

Splicing

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs886058000; hg19: chr3-132400102; API