19-55014192-C-CGGGA
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 2P and 10B. PVS1_ModerateBP6_ModerateBS1BS2
The NM_001083899.2(GP6):c.1752_1753insTCCC(p.Gly585SerfsTer7) variant causes a frameshift change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00592 in 152,220 control chromosomes in the GnomAD database, including 11 homozygotes. Variant has been reported in ClinVar as Benign (★).
Frequency
Consequence
NM_001083899.2 frameshift
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
GP6 | ENST00000310373.7 | c.1752_1753insTCCC | p.Gly585SerfsTer7 | frameshift_variant | Exon 8 of 8 | 1 | NM_001083899.2 | ENSP00000308782.3 | ||
GP6 | ENST00000417454 | c.*728_*729insTCCC | 3_prime_UTR_variant | Exon 8 of 8 | 1 | ENSP00000394922.1 |
Frequencies
GnomAD3 genomes AF: 0.00594 AC: 903AN: 152102Hom.: 11 Cov.: 32
GnomAD3 exomes AF: 0.00125 AC: 185AN: 147996Hom.: 1 AF XY: 0.000919 AC XY: 74AN XY: 80484
GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.000722 AC: 413AN: 571810Hom.: 1 Cov.: 6 AF XY: 0.000543 AC XY: 168AN XY: 309542
GnomAD4 genome AF: 0.00592 AC: 901AN: 152220Hom.: 11 Cov.: 32 AF XY: 0.00585 AC XY: 435AN XY: 74420
ClinVar
Submissions by phenotype
GP6-related disorder Benign:1
This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -
not provided Benign:1
- -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at