7-6463130-G-A
Variant summary
Our verdict is Benign. Variant got -7 ACMG points: 2P and 9B. PM2BP4_StrongBP6BS1
The ENST00000490996.1(KDELR2):c.397C>T(p.Pro133Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000101 in 1,614,126 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 10/14 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (no stars).
Frequency
Consequence
ENST00000490996.1 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -7 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
KDELR2 | NM_006854.4 | c.*11C>T | 3_prime_UTR_variant | 5/5 | ENST00000258739.9 | NP_006845.1 | ||
KDELR2 | NM_001100603.2 | c.397C>T | p.Pro133Ser | missense_variant | 4/4 | NP_001094073.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
KDELR2 | ENST00000258739.9 | c.*11C>T | 3_prime_UTR_variant | 5/5 | 1 | NM_006854.4 | ENSP00000258739 | P1 |
Frequencies
GnomAD3 genomes AF: 0.000138 AC: 21AN: 152160Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000398 AC: 100AN: 251256Hom.: 0 AF XY: 0.000324 AC XY: 44AN XY: 135840
GnomAD4 exome AF: 0.0000958 AC: 140AN: 1461848Hom.: 1 Cov.: 31 AF XY: 0.0000963 AC XY: 70AN XY: 727226
GnomAD4 genome AF: 0.000151 AC: 23AN: 152278Hom.: 0 Cov.: 32 AF XY: 0.000161 AC XY: 12AN XY: 74458
ClinVar
Submissions by phenotype
KDELR2-related disorder Benign:1
Likely benign, no assertion criteria provided | clinical testing | PreventionGenetics, part of Exact Sciences | Nov 08, 2023 | 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