chr2-27497335-G-A
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_StrongBP6_Moderate
The NM_001486.4(GCKR):c.152G>A(p.Arg51Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000406 in 1,614,030 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Consequence
NM_001486.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GCKR | NM_001486.4 | c.152G>A | p.Arg51Gln | missense_variant | 2/19 | ENST00000264717.7 | |
GCKR | XM_011532763.1 | c.152G>A | p.Arg51Gln | missense_variant | 2/13 | ||
GCKR | XR_001738699.1 | n.218G>A | non_coding_transcript_exon_variant | 2/13 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GCKR | ENST00000264717.7 | c.152G>A | p.Arg51Gln | missense_variant | 2/19 | 1 | NM_001486.4 | P1 | |
GCKR | ENST00000472290.1 | n.174G>A | non_coding_transcript_exon_variant | 2/11 | 1 | ||||
GCKR | ENST00000453813.1 | c.68G>A | p.Arg23Gln | missense_variant | 1/8 | 3 | |||
GCKR | ENST00000417872.5 | n.209G>A | non_coding_transcript_exon_variant | 2/7 | 4 |
Frequencies
GnomAD3 genomes ? AF: 0.000256 AC: 39AN: 152158Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000410 AC: 103AN: 251490Hom.: 1 AF XY: 0.000368 AC XY: 50AN XY: 135920
GnomAD4 exome AF: 0.000422 AC: 617AN: 1461872Hom.: 2 Cov.: 32 AF XY: 0.000404 AC XY: 294AN XY: 727234
GnomAD4 genome ? AF: 0.000256 AC: 39AN: 152158Hom.: 0 Cov.: 32 AF XY: 0.000175 AC XY: 13AN XY: 74334
ClinVar
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Sep 26, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at