rs200896335

Variant names:

• chr10-101010536-TGCTGCGGCTGCG-T
• rs200896335
• NM_001195263.2:c.2341_2352delCGCAGCCGCAGC

Your query was ambiguous. Multiple possible variants found:

• chr10-101010536-TGCTGCGGCTGCG-T
• chr10-101010536-TGCTGCGGCTGCG-TGCTGCG
• chr10-101010536-TGCTGCGGCTGCG-TGCTGCGGCTGCGGCTGCG
• chr10-101010536-TGCTGCGGCTGCG-TGCTGCGGCTGCGGCTGCGGCTGCGGCTACGGCTGCGGCTGCGGCTGCG
• chr10-101010536-TGCTGCGGCTGCG-TGCTGCGGCTGCGGCTGCGGCTGCG
• chr10-101010536-TGCTGCGGCTGCG-TGCTGCGGCTGCGGCTGCGGCTGCGGCTGCG

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.2341_2352delCGCAGCCGCAGC​(p.Arg781_Ser784del) variant causes a conservative inframe deletion change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000315 in 1,523,836 control chromosomes in the GnomAD database, with no homozygous occurrence. 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 (★★).

• Frequency:
  • Genomes: 𝑓 0.000079 (0 hom., cov: 0)
  • Exomes 𝑓: 0.000026 (0 hom.)
• Consequence: PDZD7 NM_001195263.2 conservative_inframe_deletion
• Clinical Significance: Likely benign criteria provided, multiple submitters, no conflicts B:2
• Conservation: PhyloP100: 0.894
• Publications: 10 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: AR Classification: DEFINITIVE Submitted by: ClinGen
• hearing loss, autosomal recessive 57

  Inheritance: AR Classification: STRONG Submitted by: PanelApp Australia, 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 10-101010536-TGCTGCGGCTGCG-T is Benign according to our data. Variant chr10-101010536-TGCTGCGGCTGCG-T is described in ClinVar as Likely_benign. ClinVar VariationId is 1051760.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PDZD7	NM_001195263.2	c.2341_2352delCGCAGCCGCAGC	p.Arg781_Ser784del	conservative_inframe_deletion	Exon 15 of 17	ENST00000619208.6	NP_001182192.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PDZD7	ENST00000619208.6	c.2341_2352delCGCAGCCGCAGC	p.Arg781_Ser784del	conservative_inframe_deletion	Exon 15 of 17	5	NM_001195263.2	ENSP00000480489.1
PDZD7	ENST00000474125.7	n.*2288_*2299delCGCAGCCGCAGC		non_coding_transcript_exon_variant	Exon 11 of 13	2		ENSP00000474447.1
PDZD7	ENST00000474125.7	n.*2288_*2299delCGCAGCCGCAGC		3_prime_UTR_variant	Exon 11 of 13	2		ENSP00000474447.1

Frequencies

GnomAD3 genomes AF: 0.0000793 AC: 12 AN: 151384 Hom.: 0 Cov.: 0

Gnomad AFR AF: 0.000218

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.000208

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0000295

Gnomad OTH AF: 0.00

GnomAD2 exomes AF: 0.0000311 AC: 4 AN: 128718 AF XY: 0.0000430

Gnomad AFR exome AF: 0.000312

Gnomad AMR exome AF: 0.00

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.00

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.0000201

Gnomad OTH exome AF: 0.00

GnomAD4 exome AF: 0.0000262 AC: 36 AN: 1372452 Hom.: 0 AF XY: 0.0000252 AC XY: 17 AN XY: 675328

African (AFR) AF: 0.000287 AC: 9 AN: 31396

American (AMR) AF: 0.00 AC: 0 AN: 35320

Ashkenazi Jewish (ASJ) AF: 0.0000407 AC: 1 AN: 24592

East Asian (EAS) AF: 0.00 AC: 0 AN: 35512

South Asian (SAS) AF: 0.0000128 AC: 1 AN: 78340

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 33538

Middle Eastern (MID) AF: 0.000179 AC: 1 AN: 5594

European-Non Finnish (NFE) AF: 0.0000205 AC: 22 AN: 1070814

Other (OTH) AF: 0.0000349 AC: 2 AN: 57346

GnomAD4 genome AF: 0.0000793 AC: 12 AN: 151384 Hom.: 0 Cov.: 0 AF XY: 0.0000406 AC XY: 3 AN XY: 73840

African (AFR) AF: 0.000218 AC: 9 AN: 41280

American (AMR) AF: 0.00 AC: 0 AN: 15214

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3460

East Asian (EAS) AF: 0.00 AC: 0 AN: 5180

South Asian (SAS) AF: 0.000208 AC: 1 AN: 4806

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 10446

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 316

European-Non Finnish (NFE) AF: 0.0000295 AC: 2 AN: 67706

Other (OTH) AF: 0.00 AC: 0 AN: 2076

Alfa AF: 0.0000546 Hom.: 1561

ClinVar

Significance: Likely benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

not provided Benign:2

Jan 23, 2025

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Likely benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Mar 06, 2020

GeneDx

Significance: Likely benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This variant is associated with the following publications: (PMID: 31129248) -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
PhyloP100		0.89

Splicing

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

Other links and lift over

dbSNP: rs200896335; hg19: chr10-102770293;