14-103562952-G-T
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The ENST00000557172.5(KLC1):c.-2+968G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00599 in 1,440,974 control chromosomes in the GnomAD database, including 49 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Consequence
ENST00000557172.5 intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
COA8 | NM_001370595.2 | c.-50G>T | upstream_gene_variant | ENST00000409074.8 | NP_001357524.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
COA8 | ENST00000409074.8 | c.-50G>T | upstream_gene_variant | 1 | NM_001370595.2 | ENSP00000386485.3 | ||||
ENSG00000256500 | ENST00000472726.3 | c.-50G>T | upstream_gene_variant | 2 | ENSP00000439065.2 |
Frequencies
GnomAD3 genomes AF: 0.00539 AC: 820AN: 152144Hom.: 1 Cov.: 34
GnomAD3 exomes AF: 0.00832 AC: 477AN: 57338Hom.: 10 AF XY: 0.00854 AC XY: 279AN XY: 32680
GnomAD4 exome AF: 0.00606 AC: 7816AN: 1288718Hom.: 48 Cov.: 32 AF XY: 0.00638 AC XY: 4022AN XY: 630028
GnomAD4 genome AF: 0.00539 AC: 821AN: 152256Hom.: 1 Cov.: 34 AF XY: 0.00545 AC XY: 406AN XY: 74436
ClinVar
Submissions by phenotype
not specified Benign:1
This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at