chr6-75922158-A-G
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Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 2P and 7B. PM2BP4_StrongBP6_ModerateBP7
The NM_001563.4(IMPG1):āc.2325T>Cā(p.Ser775=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000131 in 152,262 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (ā ).
Frequency
Genomes: š 0.000013 ( 0 hom., cov: 32)
Exomes š: 8.6e-7 ( 0 hom. )
Failed GnomAD Quality Control
Consequence
IMPG1
NM_001563.4 synonymous
NM_001563.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.123
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 -5 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.81).
BP6
Variant 6-75922158-A-G is Benign according to our data. Variant chr6-75922158-A-G is described in ClinVar as [Likely_benign]. Clinvar id is 1131043.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=0.123 with no splicing effect.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
IMPG1 | NM_001563.4 | c.2325T>C | p.Ser775= | synonymous_variant | 17/17 | ENST00000369950.8 | |
IMPG1 | NM_001282368.2 | c.2091T>C | p.Ser697= | synonymous_variant | 16/16 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
IMPG1 | ENST00000369950.8 | c.2325T>C | p.Ser775= | synonymous_variant | 17/17 | 1 | NM_001563.4 | P2 | |
IMPG1 | ENST00000611179.4 | c.2091T>C | p.Ser697= | synonymous_variant | 16/16 | 5 | A2 | ||
IMPG1 | ENST00000369952.3 | c.408T>C | p.Ser136= | synonymous_variant | 4/4 | 3 |
Frequencies
GnomAD3 genomes AF: 0.0000131 AC: 2AN: 152144Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.00000506 AC: 1AN: 197502Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 105234
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GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 8.61e-7 AC: 1AN: 1162070Hom.: 0 Cov.: 16 AF XY: 0.00000170 AC XY: 1AN XY: 587140
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GnomAD4 genome AF: 0.0000131 AC: 2AN: 152262Hom.: 0 Cov.: 32 AF XY: 0.0000134 AC XY: 1AN XY: 74444
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Sep 04, 2020 | - - |
Computational scores
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Benign
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Benign
DANN
Benign
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at