12-75503942-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_007043.7(KRR1):c.793G>A(p.Glu265Lys) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000267 in 1,611,880 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_007043.7 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
KRR1 | NM_007043.7 | c.793G>A | p.Glu265Lys | missense_variant | Exon 7 of 10 | ENST00000229214.9 | NP_008974.5 | |
KRR1 | XM_047428133.1 | c.499G>A | p.Glu167Lys | missense_variant | Exon 7 of 10 | XP_047284089.1 | ||
GLIPR1 | NM_006851.3 | c.*4964C>T | downstream_gene_variant | ENST00000266659.8 | NP_006842.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
KRR1 | ENST00000229214.9 | c.793G>A | p.Glu265Lys | missense_variant | Exon 7 of 10 | 1 | NM_007043.7 | ENSP00000229214.4 | ||
KRR1 | ENST00000438169.6 | c.660+1256G>A | intron_variant | Intron 6 of 8 | 1 | ENSP00000411740.2 | ||||
KRR1 | ENST00000551070.5 | n.341G>A | non_coding_transcript_exon_variant | Exon 1 of 4 | 2 | |||||
GLIPR1 | ENST00000266659.8 | c.*4964C>T | downstream_gene_variant | 1 | NM_006851.3 | ENSP00000266659.3 |
Frequencies
GnomAD3 genomes AF: 0.0000197 AC: 3AN: 151932Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000159 AC: 4AN: 250950Hom.: 0 AF XY: 0.00000737 AC XY: 1AN XY: 135648
GnomAD4 exome AF: 0.0000274 AC: 40AN: 1459948Hom.: 0 Cov.: 30 AF XY: 0.0000262 AC XY: 19AN XY: 726270
GnomAD4 genome AF: 0.0000197 AC: 3AN: 151932Hom.: 0 Cov.: 32 AF XY: 0.0000270 AC XY: 2AN XY: 74208
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.793G>A (p.E265K) alteration is located in exon 7 (coding exon 7) of the KRR1 gene. This alteration results from a G to A substitution at nucleotide position 793, causing the glutamic acid (E) at amino acid position 265 to be replaced by a lysine (K). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at