rs749159571
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP6
The NM_006854.4(KDELR2):c.*177_*178delGC variant causes a 3 prime UTR change. The variant allele was found at a frequency of 0.0000919 in 1,609,584 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Likely benign (no stars).
Frequency
Consequence
NM_006854.4 3_prime_UTR
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
KDELR2 | NM_006854.4 | c.*177_*178delGC | 3_prime_UTR_variant | Exon 5 of 5 | ENST00000258739.9 | NP_006845.1 | ||
KDELR2 | NM_001100603.2 | c.*2_*3delGC | 3_prime_UTR_variant | Exon 4 of 4 | NP_001094073.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000545 AC: 83AN: 152218Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000155 AC: 38AN: 245920Hom.: 0 AF XY: 0.000112 AC XY: 15AN XY: 133362
GnomAD4 exome AF: 0.0000439 AC: 64AN: 1457248Hom.: 0 AF XY: 0.0000386 AC XY: 28AN XY: 724820
GnomAD4 genome AF: 0.000551 AC: 84AN: 152336Hom.: 0 Cov.: 32 AF XY: 0.000604 AC XY: 45AN XY: 74500
ClinVar
Submissions by phenotype
KDELR2-related disorder Benign:1
This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at