10-101012526-A-C

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_001195263.2(PDZD7):​c.1750-268T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.482 in 152,052 control chromosomes in the GnomAD database, including 20,749 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.48 ( 20749 hom., cov: 33)

Consequence

PDZD7
NM_001195263.2 intron

Scores

2

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: 0.237
Variant links:
Genes affected
PDZD7 (HGNC:26257): (PDZ domain containing 7) This gene encodes a ciliary protein homologous to proteins which are mutated in Usher syndrome patients, and mutations and translocations involving this gene have been associated with two types of Usher syndrome. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Dec 2010]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.85).
BP6
Variant 10-101012526-A-C is Benign according to our data. Variant chr10-101012526-A-C is described in ClinVar as [Benign]. Clinvar id is 683852.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.642 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
PDZD7NM_001195263.2 linkuse as main transcriptc.1750-268T>G intron_variant ENST00000619208.6 NP_001182192.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
PDZD7ENST00000619208.6 linkuse as main transcriptc.1750-268T>G intron_variant 5 NM_001195263.2 ENSP00000480489 P1Q9H5P4-3
PDZD7ENST00000644782.1 linkuse as main transcriptc.1523-268T>G intron_variant ENSP00000496747
PDZD7ENST00000474125.7 linkuse as main transcriptc.*1701-268T>G intron_variant, NMD_transcript_variant 2 ENSP00000474447

Frequencies

GnomAD3 genomes
AF:
0.482
AC:
73258
AN:
151934
Hom.:
20753
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.208
Gnomad AMI
AF:
0.630
Gnomad AMR
AF:
0.521
Gnomad ASJ
AF:
0.616
Gnomad EAS
AF:
0.0899
Gnomad SAS
AF:
0.406
Gnomad FIN
AF:
0.600
Gnomad MID
AF:
0.604
Gnomad NFE
AF:
0.647
Gnomad OTH
AF:
0.511
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.482
AC:
73265
AN:
152052
Hom.:
20749
Cov.:
33
AF XY:
0.477
AC XY:
35446
AN XY:
74298
show subpopulations
Gnomad4 AFR
AF:
0.207
Gnomad4 AMR
AF:
0.520
Gnomad4 ASJ
AF:
0.616
Gnomad4 EAS
AF:
0.0901
Gnomad4 SAS
AF:
0.406
Gnomad4 FIN
AF:
0.600
Gnomad4 NFE
AF:
0.647
Gnomad4 OTH
AF:
0.507
Alfa
AF:
0.602
Hom.:
37579
Bravo
AF:
0.462
Asia WGS
AF:
0.248
AC:
864
AN:
3478

ClinVar

Significance: Benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link

Submissions by phenotype

not provided Benign:2
Benign, criteria provided, single submitterclinical testingGeneDxJun 14, 2018This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. -
Benign, criteria provided, single submitternot providedBreakthrough Genomics, Breakthrough Genomics-- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.85
CADD
Benign
4.9
DANN
Benign
0.68

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: rs11190790; hg19: chr10-102772283; API