chr4-849932-T-C
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_005255.4(GAK):āc.3794A>Gā(p.Lys1265Arg) variant causes a missense change. The variant allele was found at a frequency of 0.0408 in 1,603,568 control chromosomes in the GnomAD database, including 1,694 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Consequence
NM_005255.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GAK | NM_005255.4 | c.3794A>G | p.Lys1265Arg | missense_variant | 27/28 | ENST00000314167.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GAK | ENST00000314167.9 | c.3794A>G | p.Lys1265Arg | missense_variant | 27/28 | 1 | NM_005255.4 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0354 AC: 5278AN: 149108Hom.: 126 Cov.: 32
GnomAD3 exomes AF: 0.0431 AC: 10570AN: 245508Hom.: 312 AF XY: 0.0438 AC XY: 5850AN XY: 133542
GnomAD4 exome AF: 0.0413 AC: 60067AN: 1454352Hom.: 1567 Cov.: 35 AF XY: 0.0414 AC XY: 29948AN XY: 723376
GnomAD4 genome AF: 0.0354 AC: 5279AN: 149216Hom.: 127 Cov.: 32 AF XY: 0.0365 AC XY: 2653AN XY: 72698
ClinVar
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Feb 24, 2021 | This variant is associated with the following publications: (PMID: 26676575) - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at