6-75923627-A-AT
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Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 0P and 2B. BP6_Moderate
The NM_001563.4(IMPG1):c.2316+6_2316+7insA variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000106 in 1,420,432 control chromosomes in the GnomAD database, with no homozygous occurrence. 1/1 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.000053 ( 0 hom., cov: 32)
Exomes 𝑓: 0.0000055 ( 0 hom. )
Consequence
IMPG1
NM_001563.4 splice_region, intron
NM_001563.4 splice_region, intron
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: -1.32
Genes affected
IMPG1 (HGNC:6055): (interphotoreceptor matrix proteoglycan 1) This gene encodes a protein that is a major component of the retinal interphotoreceptor matrix. The encoded protein is a proteoglycan that is thought to play a role in maintaining viability of photoreceptor cells and in adhesion of the neural retina to the retinal pigment epithelium. Alternate splicing results in multiple transcript variants. [provided by RefSeq, Sep 2013]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -2 ACMG points.
BP6
Variant 6-75923627-A-AT is Benign according to our data. Variant chr6-75923627-A-AT is described in ClinVar as [Benign]. Clinvar id is 1169591.Status of the report is criteria_provided_single_submitter, 1 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
IMPG1 | NM_001563.4 | c.2316+6_2316+7insA | splice_region_variant, intron_variant | ENST00000369950.8 | |||
IMPG1 | NM_001282368.2 | c.2082+6_2082+7insA | splice_region_variant, intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
IMPG1 | ENST00000369950.8 | c.2316+6_2316+7insA | splice_region_variant, intron_variant | 1 | NM_001563.4 | P2 | |||
IMPG1 | ENST00000369952.3 | c.399+6_399+7insA | splice_region_variant, intron_variant | 3 | |||||
IMPG1 | ENST00000611179.4 | c.2082+6_2082+7insA | splice_region_variant, intron_variant | 5 | A2 |
Frequencies
GnomAD3 genomes AF: 0.0000526 AC: 8AN: 152116Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.0000212 AC: 5AN: 235480Hom.: 0 AF XY: 0.0000158 AC XY: 2AN XY: 126670
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GnomAD4 exome AF: 0.00000552 AC: 7AN: 1268316Hom.: 0 Cov.: 18 AF XY: 0.00000469 AC XY: 3AN XY: 639648
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GnomAD4 genome AF: 0.0000526 AC: 8AN: 152116Hom.: 0 Cov.: 32 AF XY: 0.0000404 AC XY: 3AN XY: 74318
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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 submitter | clinical testing | Invitae | Jan 15, 2024 | - - |
Computational scores
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Find out detailed SpliceAI scores and Pangolin per-transcript scores at