22-19180775-C-T
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The NM_007098.4(CLTCL1):c.4859G>A(p.Arg1620His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00929 in 1,613,786 control chromosomes in the GnomAD database, including 192 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Consequence
NM_007098.4 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CLTCL1 | NM_007098.4 | c.4859G>A | p.Arg1620His | missense_variant | 31/33 | ENST00000427926.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CLTCL1 | ENST00000427926.6 | c.4859G>A | p.Arg1620His | missense_variant | 31/33 | 1 | NM_007098.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00725 AC: 1103AN: 152198Hom.: 17 Cov.: 34
GnomAD3 exomes AF: 0.0119 AC: 2961AN: 249178Hom.: 59 AF XY: 0.0140 AC XY: 1893AN XY: 135204
GnomAD4 exome AF: 0.00950 AC: 13886AN: 1461470Hom.: 175 Cov.: 31 AF XY: 0.0107 AC XY: 7747AN XY: 727030
GnomAD4 genome ? AF: 0.00722 AC: 1099AN: 152316Hom.: 17 Cov.: 34 AF XY: 0.00769 AC XY: 573AN XY: 74494
ClinVar
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Feb 01, 2023 | CLTCL1: BP4, BS1, BS2 - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at