rs10418074
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_001083899.2(GP6):c.1727G>A(p.Arg576Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0543 in 793,436 control chromosomes in the GnomAD database, including 1,362 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/17 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_001083899.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GP6 | NM_001083899.2 | c.1727G>A | p.Arg576Lys | missense_variant | 8/8 | ENST00000310373.7 | |
GP6-AS1 | XR_001754012.3 | n.121+7754C>T | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GP6 | ENST00000310373.7 | c.1727G>A | p.Arg576Lys | missense_variant | 8/8 | 1 | NM_001083899.2 | ||
GP6-AS1 | ENST00000593060.5 | n.155+7754C>T | intron_variant, non_coding_transcript_variant | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.0650 AC: 9878AN: 152074Hom.: 388 Cov.: 32
GnomAD3 exomes AF: 0.0519 AC: 9410AN: 181162Hom.: 296 AF XY: 0.0530 AC XY: 5259AN XY: 99258
GnomAD4 exome AF: 0.0518 AC: 33223AN: 641244Hom.: 975 Cov.: 8 AF XY: 0.0524 AC XY: 18133AN XY: 345768
GnomAD4 genome ? AF: 0.0649 AC: 9879AN: 152192Hom.: 387 Cov.: 32 AF XY: 0.0642 AC XY: 4779AN XY: 74400
ClinVar
Submissions by phenotype
not provided Benign:2
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 31, 2024 | - - |
Benign, criteria provided, single submitter | clinical testing | GeneDx | Nov 12, 2018 | - - |
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | - | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at