12-66347521-A-AATT
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BS1_Supporting
The NM_001366722.1(GRIP1):c.*1495_*1497dupAAT variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000171 in 152,340 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: 𝑓 0.00017 ( 0 hom., cov: 33)
Exomes 𝑓: 0.0 ( 0 hom. )
Failed GnomAD Quality Control
Consequence
GRIP1
NM_001366722.1 3_prime_UTR
NM_001366722.1 3_prime_UTR
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 3.48
Genes affected
GRIP1 (HGNC:18708): (glutamate receptor interacting protein 1) This gene encodes a member of the glutamate receptor interacting protein family. The encoded scaffold protein binds to and mediates the trafficking and membrane organization of a number of transmembrane proteins. Alternatively spliced transcript variants encoding different isoforms have been described. [provided by RefSeq, May 2010]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 1 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BS1
Variant frequency is greater than expected in population eas. gnomad4 allele frequency = 0.000171 (26/152340) while in subpopulation EAS AF= 0.00482 (25/5186). AF 95% confidence interval is 0.00335. There are 0 homozygotes in gnomad4. There are 14 alleles in male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck. Existence of Clinvar submissions makes me limit the strength of this signal to Supporting
Transcripts
RefSeq
| Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|
| GRIP1 | NM_001366722.1 | c.*1495_*1497dupAAT | 3_prime_UTR_variant | Exon 25 of 25 | ENST00000359742.9 | NP_001353651.1 |
Ensembl
| Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
|---|---|---|---|---|---|---|---|---|---|---|
| GRIP1 | ENST00000359742 | c.*1495_*1497dupAAT | 3_prime_UTR_variant | Exon 25 of 25 | 5 | NM_001366722.1 | ENSP00000352780.4 | |||
| GRIP1 | ENST00000398016 | c.*1495_*1497dupAAT | 3_prime_UTR_variant | Exon 24 of 24 | 1 | ENSP00000381098.3 | ||||
| GRIP1 | ENST00000696989.1 | c.*1495_*1497dupAAT | downstream_gene_variant | ENSP00000513025.1 |
Frequencies
GnomAD3 genomes 0.000171 AC: 26AN: 152222Hom.: 0 Cov.: 33
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GnomAD4 exome Data not reliable, filtered out with message: AC0;AS_VQSR AF: 0.00 AC: 0AN: 2Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0AN XY: 2
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Data not reliable, filtered out with message: AC0;AS_VQSR
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GnomAD4 genome 0.000171 AC: 26AN: 152340Hom.: 0 Cov.: 33 AF XY: 0.000188 AC XY: 14AN XY: 74500
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3478
ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Fraser syndrome 1 Uncertain:1
Jun 14, 2016
Illumina Laboratory Services, Illumina
Significance: Uncertain significance
Review Status: criteria provided, single submitter
Collection Method: clinical testing
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Computational scores
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Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at