chr10-101008496-TAGAATC-T

Position:

• chr10-101008496-TAGAATC-T

Variant summary

Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PM2 PM4

The NM_001195263.2(PDZD7):​c.3067_3072delGATTCT​(p.Asp1023_Ser1024del) variant causes a conservative inframe deletion change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000102 in 1,377,666 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).

• Frequency:
  • Genomes: not found (cov: 30)
  • Exomes 𝑓: 0.000010 (0 hom.)
• Consequence: PDZD7 NM_001195263.2 conservative_inframe_deletion
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1
• Conservation: PhyloP100: -0.282

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]

ACMG classification

Verdict is Uncertain_significance. Variant got 4 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• PM4: Nonframeshift variant in NON repetitive region in NM_001195263.2.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PDZD7	NM_001195263.2	c.3067_3072delGATTCT	p.Asp1023_Ser1024del	conservative_inframe_deletion	17/17	ENST00000619208.6	NP_001182192.1
PDZD7	XM_011540177.4	c.3067_3072delGATTCT	p.Asp1023_Ser1024del	conservative_inframe_deletion	18/18		XP_011538479.1
PDZD7	XM_047425767.1	c.3067_3072delGATTCT	p.Asp1023_Ser1024del	conservative_inframe_deletion	17/17		XP_047281723.1
PDZD7	XM_011540178.4	c.3064_3069delGATTCT	p.Asp1022_Ser1023del	conservative_inframe_deletion	17/17		XP_011538480.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PDZD7	ENST00000619208.6	c.3067_3072delGATTCT	p.Asp1023_Ser1024del	conservative_inframe_deletion	17/17	5	NM_001195263.2	ENSP00000480489.1
PDZD7	ENST00000474125.7	n.*3014_*3019delGATTCT		non_coding_transcript_exon_variant	13/13	2		ENSP00000474447.1
PDZD7	ENST00000474125.7	n.*3014_*3019delGATTCT		3_prime_UTR_variant	13/13	2		ENSP00000474447.1

Frequencies

GnomAD3 genomes Cov.: 30

GnomAD3 exomes AF: 0.00000754 AC: 1 AN: 132594 Hom.: 0 AF XY: 0.0000140 AC XY: 1 AN XY: 71476

Gnomad AFR exome AF: 0.00

Gnomad AMR exome AF: 0.00

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.00

Gnomad SAS exome AF: 0.00

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.0000192

Gnomad OTH exome AF: 0.00

GnomAD4 exome AF: 0.0000102 AC: 14 AN: 1377666 Hom.: 0 AF XY: 0.00000442 AC XY: 3 AN XY: 678984

Gnomad4 AFR exome AF: 0.0000318

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.0000121

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome Cov.: 30

Bravo AF: 0.00000756

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

GeneDx

Apr 20, 2021

Not observed at a significant frequency in large population cohorts (Lek et al., 2016); In-frame deletion of 2 amino acids in a non-repeat region; In silico analysis supports that this variant does not alter protein structure/function; Has not been previously published as pathogenic or benign to our knowledge -

Computational scores

Source: dbNSFP v4.3

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs962387635; hg19: chr10-102768253;