rs1654416
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001083899.2(GP6):āc.709G>Cā(p.Glu237Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000025 in 1,600,792 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. E237K) has been classified as Benign.
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.709G>C | p.Glu237Gln | missense_variant | 6/8 | ENST00000310373.7 | |
GP6-AS1 | XR_001754012.3 | n.121+12203C>G | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GP6 | ENST00000310373.7 | c.709G>C | p.Glu237Gln | missense_variant | 6/8 | 1 | NM_001083899.2 | ||
GP6-AS1 | ENST00000593060.5 | n.155+12203C>G | intron_variant, non_coding_transcript_variant | 5 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152110Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.00000401 AC: 1AN: 249554Hom.: 0 AF XY: 0.00000739 AC XY: 1AN XY: 135398
GnomAD4 exome AF: 0.00000207 AC: 3AN: 1448682Hom.: 0 Cov.: 30 AF XY: 0.00000416 AC XY: 3AN XY: 721496
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152110Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 74302
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at