chr19-55014322-C-T
Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP6_Very_StrongBP7
The NM_001083899.2(GP6):c.1623G>A(p.Leu541=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000129 in 1,591,024 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★). Synonymous variant affecting the same amino acid position (i.e. L541L) has been classified as Likely benign.
Frequency
Consequence
NM_001083899.2 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -13 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GP6 | NM_001083899.2 | c.1623G>A | p.Leu541= | synonymous_variant | 8/8 | ENST00000310373.7 | |
GP6-AS1 | XR_001754012.3 | n.121+7858C>T | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GP6 | ENST00000310373.7 | c.1623G>A | p.Leu541= | synonymous_variant | 8/8 | 1 | NM_001083899.2 | ||
GP6-AS1 | ENST00000593060.5 | n.155+7858C>T | intron_variant, non_coding_transcript_variant | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.000125 AC: 19AN: 152128Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000387 AC: 95AN: 245790Hom.: 0 AF XY: 0.000352 AC XY: 47AN XY: 133560
GnomAD4 exome AF: 0.000130 AC: 187AN: 1438778Hom.: 2 Cov.: 28 AF XY: 0.000139 AC XY: 100AN XY: 717312
GnomAD4 genome ? AF: 0.000125 AC: 19AN: 152246Hom.: 0 Cov.: 33 AF XY: 0.000188 AC XY: 14AN XY: 74442
ClinVar
Submissions by phenotype
GP6-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Feb 19, 2019 | 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 specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Women's Health and Genetics/Laboratory Corporation of America, LabCorp | Feb 17, 2022 | - - |
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Oct 14, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at