chr11-14469353-C-T
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP4BS2
The NM_001144061.2(COPB1):c.1948G>A(p.Glu650Lys) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000143 in 1,613,716 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_001144061.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
COPB1 | NM_001144061.2 | c.1948G>A | p.Glu650Lys | missense_variant | Exon 15 of 22 | ENST00000439561.7 | NP_001137533.1 | |
COPB1 | NM_001144062.2 | c.1948G>A | p.Glu650Lys | missense_variant | Exon 15 of 22 | NP_001137534.1 | ||
COPB1 | NM_016451.5 | c.1948G>A | p.Glu650Lys | missense_variant | Exon 15 of 22 | NP_057535.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
COPB1 | ENST00000439561.7 | c.1948G>A | p.Glu650Lys | missense_variant | Exon 15 of 22 | 1 | NM_001144061.2 | ENSP00000397873.2 | ||
COPB1 | ENST00000249923.7 | c.1948G>A | p.Glu650Lys | missense_variant | Exon 15 of 22 | 1 | ENSP00000249923.3 |
Frequencies
GnomAD3 genomes AF: 0.0000131 AC: 2AN: 152176Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000398 AC: 1AN: 251168Hom.: 0 AF XY: 0.00000737 AC XY: 1AN XY: 135760
GnomAD4 exome AF: 0.0000144 AC: 21AN: 1461540Hom.: 0 Cov.: 31 AF XY: 0.0000138 AC XY: 10AN XY: 727112
GnomAD4 genome AF: 0.0000131 AC: 2AN: 152176Hom.: 0 Cov.: 32 AF XY: 0.0000134 AC XY: 1AN XY: 74352
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.1948G>A (p.E650K) alteration is located in exon 15 (coding exon 14) of the COPB1 gene. This alteration results from a G to A substitution at nucleotide position 1948, causing the glutamic acid (E) at amino acid position 650 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