chr12-66347717-G-GTGA
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBS1BS2
The NM_001366722.1(GRIP1):c.*1301_*1302insTCA variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00956 in 151,606 control chromosomes in the GnomAD database, including 22 homozygotes. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.0096 ( 22 hom., cov: 33)
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: 3.22
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 Benign. Variant got -10 ACMG points.
BP6
?
Variant 12-66347717-G-GTGA is Benign according to our data. Variant chr12-66347717-G-GTGA is described in ClinVar as [Likely_benign]. Clinvar id is 310273.Status of the report is criteria_provided_single_submitter, 1 stars.
BS1
?
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.00956 (1449/151606) while in subpopulation AFR AF= 0.0339 (1400/41318). AF 95% confidence interval is 0.0324. There are 22 homozygotes in gnomad4. There are 693 alleles in male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck.
BS2
?
High Homozygotes in GnomAd at 22 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GRIP1 | NM_001366722.1 | c.*1301_*1302insTCA | 3_prime_UTR_variant | 25/25 | ENST00000359742.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GRIP1 | ENST00000359742.9 | c.*1301_*1302insTCA | 3_prime_UTR_variant | 25/25 | 5 | NM_001366722.1 | P1 | ||
GRIP1 | ENST00000398016.7 | c.*1301_*1302insTCA | 3_prime_UTR_variant | 24/24 | 1 | ||||
GRIP1 | ENST00000696989.1 | c.*1301_*1302insTCA | 3_prime_UTR_variant | 23/23 |
Frequencies
GnomAD3 genomes ? AF: 0.00955 AC: 1446AN: 151492Hom.: 22 Cov.: 33
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GnomAD4 exome Data not reliable, filtered out with message: AC0AC: 0AN: 0Hom.: 0 Cov.: 0AC XY: 0AN XY: 0
GnomAD4 exome
Data not reliable, filtered out with message: AC0
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GnomAD4 genome ? AF: 0.00956 AC: 1449AN: 151606Hom.: 22 Cov.: 33 AF XY: 0.00936 AC XY: 693AN XY: 74050
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?
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33
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Fraser syndrome 1 Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jun 14, 2016 | - - |
Computational scores
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Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at