13-70107466-T-C
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6BP7BA1
The NM_020866.3(KLHL1):āc.234A>Gā(p.Ser78Ser) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0792 in 1,613,850 control chromosomes in the GnomAD database, including 8,263 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (no stars).
Frequency
Consequence
NM_020866.3 synonymous
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 |
---|---|---|---|---|---|---|---|---|
KLHL1 | NM_020866.3 | c.234A>G | p.Ser78Ser | synonymous_variant | Exon 1 of 11 | ENST00000377844.9 | NP_065917.1 | |
KLHL1 | NM_001286725.2 | c.234A>G | p.Ser78Ser | synonymous_variant | Exon 1 of 10 | NP_001273654.1 | ||
ATXN8OS | NR_002717.3 | n.46T>C | non_coding_transcript_exon_variant | Exon 1 of 5 | ||||
ATXN8OS | NR_185842.1 | n.46T>C | non_coding_transcript_exon_variant | Exon 1 of 4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
KLHL1 | ENST00000377844.9 | c.234A>G | p.Ser78Ser | synonymous_variant | Exon 1 of 11 | 1 | NM_020866.3 | ENSP00000367075.4 | ||
KLHL1 | ENST00000545028.2 | c.234A>G | p.Ser78Ser | synonymous_variant | Exon 1 of 10 | 2 | ENSP00000439602.2 | |||
ATXN8OS | ENST00000414504.6 | n.254T>C | non_coding_transcript_exon_variant | Exon 1 of 5 | 5 | |||||
ATXN8OS | ENST00000665905.1 | n.138T>C | non_coding_transcript_exon_variant | Exon 1 of 4 |
Frequencies
GnomAD3 genomes AF: 0.119 AC: 18087AN: 151904Hom.: 1600 Cov.: 32
GnomAD3 exomes AF: 0.111 AC: 27586AN: 249300Hom.: 2302 AF XY: 0.104 AC XY: 14058AN XY: 134946
GnomAD4 exome AF: 0.0750 AC: 109658AN: 1461830Hom.: 6653 Cov.: 34 AF XY: 0.0748 AC XY: 54397AN XY: 727226
GnomAD4 genome AF: 0.119 AC: 18121AN: 152020Hom.: 1610 Cov.: 32 AF XY: 0.122 AC XY: 9084AN XY: 74294
ClinVar
Submissions by phenotype
KLHL1-related disorder Benign:1
This variant is classified as 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