rs727503369

Variant names:

• chr10-101010540-GCGGCTGCGGCTGCGGCTA-G
• rs727503369
• NM_001195263.2:c.2331_2348delTAGCCGCAGCCGCAGCCG

Your query was ambiguous. Multiple possible variants found:

• chr10-101010540-GCGGCTGCGGCTGCGGCTA-G
• chr10-101010540-GCGGCTGCGGCTGCGGCTA-GCGGCTGCGGCTGCGGCTACGGCTGCGGCTGCGGCTA

Variant summary

Our verdict is Benign. The variant received -9 ACMG points: 0P and 9B. BP3 BP6_Very_Strong

The NM_001195263.2(PDZD7):​c.2331_2348delTAGCCGCAGCCGCAGCCG​(p.Ser778_Arg783del) variant causes a disruptive inframe deletion change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. It is difficult to determine the true allele frequency of this variant because it is of type DEL_BIG, and the frequency of such variant types in population databases may be underestimated and unreliable. Variant has been reported in ClinVar as Likely benign (★★). Synonymous variant affecting the same amino acid position (i.e. R777R) has been classified as Likely benign.

• Frequency: Genomes: not found (cov: 32)
• Consequence: PDZD7 NM_001195263.2 disruptive_inframe_deletion
• Clinical Significance: Benign/Likely benign criteria provided, multiple submitters, no conflicts B:2
• Conservation: PhyloP100: 0.928
• Publications: 0 publications found

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]

PDZD7 Gene-Disease associations (from GenCC):

• hearing loss, autosomal recessive

  Inheritance: Unknown Classification: DEFINITIVE Submitted by: ClinGen
• hearing loss, autosomal recessive 57

  Inheritance: AR Classification: STRONG Submitted by: Labcorp Genetics (formerly Invitae)
• Usher syndrome type 2C

  Inheritance: Unknown Classification: LIMITED Submitted by: Labcorp Genetics (formerly Invitae)

ACMG classification

Our verdict: Benign. The variant received -9 ACMG points.

• BP3: Nonframeshift variant in repetitive region in NM_001195263.2
• BP6: Variant 10-101010540-GCGGCTGCGGCTGCGGCTA-G is Benign according to our data. Variant chr10-101010540-GCGGCTGCGGCTGCGGCTA-G is described in ClinVar as Benign/Likely_benign. ClinVar VariationId is 164938.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001195263.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PDZD7	NM_001195263.2	MANE Select	c.2331_2348delTAGCCGCAGCCGCAGCCG	p.Ser778_Arg783del	disruptive_inframe_deletion	Exon 15 of 17	NP_001182192.1	Q9H5P4-3
	PDZD7	NM_001437429.1		c.2328_2345delTAGCCGCAGCCGCAGCCG	p.Ser777_Arg782del	disruptive_inframe_deletion	Exon 15 of 17	NP_001424358.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PDZD7	ENST00000619208.6	TSL:5 MANE Select	c.2331_2348delTAGCCGCAGCCGCAGCCG	p.Ser778_Arg783del	disruptive_inframe_deletion	Exon 15 of 17	ENSP00000480489.1	Q9H5P4-3
	PDZD7	ENST00000912190.1		c.2328_2345delTAGCCGCAGCCGCAGCCG	p.Ser777_Arg782del	disruptive_inframe_deletion	Exon 15 of 17	ENSP00000582249.1
	PDZD7	ENST00000474125.7	TSL:2	n.*2278_*2295delTAGCCGCAGCCGCAGCCG		non_coding_transcript_exon	Exon 11 of 13	ENSP00000474447.1	S4R3J9

Frequencies

GnomAD3 genomes Cov.: 32

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

GnomAD4 genome Cov.: 32

ClinVar

ClinVar submissions

Significance: Benign/Likely benign

Revision: criteria provided, multiple submitters, no conflicts

Pathogenic	VUS	Benign	Condition
-	-	1	not provided (1)
-	-	1	not specified (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		0.93

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs727503369;

hg19: chr10-102770297;