rs12004
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_006855.4(KDELR3):āc.596T>Gā(p.Val199Gly) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.294 in 1,613,664 control chromosomes in the GnomAD database, including 71,264 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Consequence
NM_006855.4 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -12 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
KDELR3 | NM_006855.4 | c.596T>G | p.Val199Gly | missense_variant | 4/5 | ENST00000216014.9 | |
KDELR3 | NM_016657.3 | c.596T>G | p.Val199Gly | missense_variant | 4/4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
KDELR3 | ENST00000216014.9 | c.596T>G | p.Val199Gly | missense_variant | 4/5 | 1 | NM_006855.4 | P1 | |
KDELR3 | ENST00000409006.3 | c.596T>G | p.Val199Gly | missense_variant | 4/4 | 1 | |||
KDELR3 | ENST00000471268.1 | n.535T>G | non_coding_transcript_exon_variant | 4/5 | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.272 AC: 41282AN: 151926Hom.: 5903 Cov.: 32
GnomAD3 exomes AF: 0.288 AC: 72342AN: 251260Hom.: 10868 AF XY: 0.291 AC XY: 39591AN XY: 135820
GnomAD4 exome AF: 0.296 AC: 432963AN: 1461620Hom.: 65355 Cov.: 37 AF XY: 0.296 AC XY: 215270AN XY: 727098
GnomAD4 genome ? AF: 0.272 AC: 41316AN: 152044Hom.: 5909 Cov.: 32 AF XY: 0.273 AC XY: 20313AN XY: 74306
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at