chr19-55014200-C-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001083899.2(GP6):c.1745G>T(p.Ser582Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000239 in 586,018 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/18 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001083899.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GP6 | NM_001083899.2 | c.1745G>T | p.Ser582Ile | missense_variant | 8/8 | ENST00000310373.7 | |
GP6-AS1 | XR_001754012.3 | n.121+7736C>A | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GP6 | ENST00000310373.7 | c.1745G>T | p.Ser582Ile | missense_variant | 8/8 | 1 | NM_001083899.2 | ||
GP6-AS1 | ENST00000593060.5 | n.155+7736C>A | intron_variant, non_coding_transcript_variant | 5 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD3 exomes AF: 0.0000257 AC: 4AN: 155534Hom.: 0 AF XY: 0.0000236 AC XY: 2AN XY: 84676
GnomAD4 exome AF: 0.0000239 AC: 14AN: 586018Hom.: 0 Cov.: 6 AF XY: 0.0000221 AC XY: 7AN XY: 317018
GnomAD4 genome ? Cov.: 32
ClinVar
Submissions by phenotype
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Invitae | Aug 31, 2023 | 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. An algorithm developed to predict the effect of missense changes on protein structure and function (PolyPhen-2) suggests that this variant is likely to be disruptive. This variant has not been reported in the literature in individuals affected with GP6-related conditions. This variant is present in population databases (rs372168591, gnomAD 0.03%). This sequence change replaces serine, which is neutral and polar, with isoleucine, which is neutral and non-polar, at codon 582 of the GP6 protein (p.Ser582Ile). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at