chr19-55014086-ATCAGGGTAATTGACATAT-A
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP3BS1_Supporting
The NM_001083899.2(GP6):c.1841_1858delATATGTCAATTACCCTGA(p.Asn614_Leu619del) variant causes a disruptive inframe deletion change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000398 in 653,734 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001083899.2 disruptive_inframe_deletion
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
GP6 | ENST00000310373.7 | c.1841_1858delATATGTCAATTACCCTGA | p.Asn614_Leu619del | disruptive_inframe_deletion | Exon 8 of 8 | 1 | NM_001083899.2 | ENSP00000308782.3 | ||
GP6 | ENST00000417454 | c.*817_*834delATATGTCAATTACCCTGA | 3_prime_UTR_variant | Exon 8 of 8 | 1 | ENSP00000394922.1 |
Frequencies
GnomAD3 genomes AF: 0.000388 AC: 59AN: 152148Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000232 AC: 30AN: 129264Hom.: 0 AF XY: 0.000270 AC XY: 19AN XY: 70480
GnomAD4 exome AF: 0.000401 AC: 201AN: 501468Hom.: 0 AF XY: 0.000367 AC XY: 100AN XY: 272488
GnomAD4 genome AF: 0.000387 AC: 59AN: 152266Hom.: 0 Cov.: 33 AF XY: 0.000363 AC XY: 27AN XY: 74452
ClinVar
Submissions by phenotype
not provided Uncertain:1
This variant, c.1841_1858del, results in the deletion of 6 amino acid(s) of the GP6 protein (p.Asn614_Leu619del), but otherwise preserves the integrity of the reading frame. This variant is present in population databases (rs774618165, gnomAD 0.05%). This variant has not been reported in the literature in individuals affected with GP6-related conditions. ClinVar contains an entry for this variant (Variation ID: 2066876). Experimental studies and prediction algorithms are not available or were not evaluated, and the functional significance of this variant is currently unknown. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at